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/7770550/working' mkdir: created directory `/scratch/stefan/7770550/working/protonate' Storing results in /scratch/stefan/7770550/finished Working in /scratch/stefan/7770550/working /scratch/stefan/7770550/working /scratch/stefan/7770550 /scratch/stefan/7770550/working/protonate /scratch/stefan/7770550/working /scratch/stefan/7770550 Precomputing protomers for all compounds (pH: 7.4) ph 7.4: 2158 protomers created Coalesing and merging protomers 1465 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1465 protomers after new stereo-center expansion /scratch/stefan/7770550/working /scratch/stefan/7770550 Bulk generating 3D conformations all protomers in /scratch/stefan/7770550/working/3D mkdir: created directory `/scratch/stefan/7770550/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7770550/working/protonate/xaaaaaa-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' 1466 3D conformations generated for 1000 compounds Building REAL300000300001 mkdir: created directory `/scratch/stefan/7770550/working/building' mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300001' /scratch/stefan/7770550/working/building/REAL300000300001 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300001 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300001/0 /scratch/stefan/7770550/working/building/REAL300000300001 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1 `/scratch/stefan/7770550/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC(C(=O)[O-])=C1Cl) `REAL300000300001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300001 none CC1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 39, 37, 39, 39, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 41] 41 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300001 none CC1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 1, 41, 41, 41, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 22, 23, 27, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 24, 25, 26, 28, 29, 30]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300001 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300001 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `/scratch/stefan/7770550/finished' Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300001/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300001 Building REAL300000300002 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300002' /scratch/stefan/7770550/working/building/REAL300000300002 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300002 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300002/0 /scratch/stefan/7770550/working/building/REAL300000300002 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/2 `/scratch/stefan/7770550/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-]) `REAL300000300002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300002 none CCN1C=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 110, 110, 110, 96, 76, 96, 96, 32, 6, 1, 6, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 110, 183, 183, 183, 183, 183, 110, 1, 1, 1, 110] 183 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 688 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300002 none CCN1C=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 31, 99, 99, 110, 110, 110, 110, 110, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 1, 110, 110, 110, 1] 183 rigid atoms, others: [32, 1, 2, 3, 4, 5, 18, 19, 20, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300002 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300002 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300002/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300002 Building REAL300000300003 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300003' /scratch/stefan/7770550/working/building/REAL300000300003 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300003 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300003/0 /scratch/stefan/7770550/working/building/REAL300000300003 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/3 `/scratch/stefan/7770550/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C(C)=C1CC(=O)[O-]) `REAL300000300003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300003 none CC1=CC(C)=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C(C)=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 21, 24, 24, 14, 6, 1, 6, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 24, 24, 24, 24, 24] 24 rigid atoms, others: [33, 34, 35, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 55 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300003 none CC1=CC(C)=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C(C)=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 15, 20, 20, 24, 24, 24, 24, 24, 1, 1, 1, 1, 3, 4, 4, 2, 2, 2, 1, 2, 2, 2, 24, 24, 24, 2, 2, 2, 3, 3] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300003 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300003 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300003/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300003 Building REAL300000300004 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300004' /scratch/stefan/7770550/working/building/REAL300000300004 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300004 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300004/0 /scratch/stefan/7770550/working/building/REAL300000300004 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/4 `/scratch/stefan/7770550/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(Cl)=C(F)C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=C1) `REAL300000300004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300004 none O=C([O-])C1=C(F)C(Cl)=C(F)C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 16, 1, 15, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 147, 147, 147, 147, 147, 147, 92, 69, 92, 92, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 147, 1, 1, 1, 147] 147 rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 28]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300004 none O=C([O-])C1=C(F)C(Cl)=C(F)C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 16, 1, 15, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 60, 115, 115, 147, 147, 147, 147, 147, 1, 145, 147, 147, 1] 147 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 28] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300004 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300004 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300004/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300004 Building REAL300000300005 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300005' /scratch/stefan/7770550/working/building/REAL300000300005 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300005 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300005/0 /scratch/stefan/7770550/working/building/REAL300000300005 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/5 `/scratch/stefan/7770550/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-]) `REAL300000300005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300005 none CC1=C(Cl)C=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 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, 53, 49, 53, 53, 26, 6, 1, 6, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 55] 55 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300005 none CC1=C(Cl)C=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 19, 52, 52, 55, 55, 55, 55, 55, 1, 1, 1, 3, 3, 2, 2, 2, 1, 55, 55, 55, 1] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300005 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300005 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300005/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300005 Building REAL300000300006 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300006' /scratch/stefan/7770550/working/building/REAL300000300006 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300006 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300006/0 /scratch/stefan/7770550/working/building/REAL300000300006 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/6 `/scratch/stefan/7770550/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C(C(=O)[O-])S1) `REAL300000300006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300006 none CC(C)(C)C1=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 51, 38, 51, 51, 21, 12, 1, 12, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 55] 55 rigid atoms, others: [34, 35, 36, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300006 none CC(C)(C)C1=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 9, 33, 50, 50, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 55, 55, 55, 1] 55 rigid atoms, others: [1, 4, 5, 6, 19, 20, 21, 22, 23, 24, 37] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300006 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300006 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300006/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300006 Building REAL300000300007 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300007' /scratch/stefan/7770550/working/building/REAL300000300007 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300007 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300007/0 /scratch/stefan/7770550/working/building/REAL300000300007 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/7 `/scratch/stefan/7770550/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-]) `REAL300000300007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300007 none COC1=CC(Cl)=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 99, 99, 99, 99, 99, 98, 61, 98, 98, 43, 13, 1, 13, 1, 1, 1, 1, 1, 1, 99, 99, 99, 107, 107, 107, 107, 107, 99, 1, 1, 1, 99] 107 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300007 none COC1=CC(Cl)=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 31, 66, 66, 99, 99, 99, 99, 99, 1, 1, 1, 3, 3, 3, 3, 3, 1, 99, 99, 99, 1] 107 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300007 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300007 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300007/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300007 Building REAL300000300008 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300008' /scratch/stefan/7770550/working/building/REAL300000300008 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300008 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300008/0 /scratch/stefan/7770550/working/building/REAL300000300008 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/8 `/scratch/stefan/7770550/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC=C1C(=O)[O-]) `REAL300000300008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300008 none CC1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 80, 111, 111, 38, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 201, 201] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 458 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300008 none CC1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 45, 171, 171, 201, 201, 201, 201, 201, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 26, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300008 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300008 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300008/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300008 Building REAL300000300009 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300009' /scratch/stefan/7770550/working/building/REAL300000300009 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300009 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300009/0 /scratch/stefan/7770550/working/building/REAL300000300009 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/9 `/scratch/stefan/7770550/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C([N+](=O)[O-])=C1) `REAL300000300009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300009 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 42, 54, 54, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1, 1, 54] 54 rigid atoms, others: [32, 13, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300009 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 20, 42, 42, 54, 54, 54, 54, 54, 1, 1, 2, 2, 1, 2, 2, 1, 1, 54, 54, 54, 1] 54 rigid atoms, others: [33, 3, 4, 5, 6, 7, 8, 21, 22, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 26, 27, 30, 31, 32]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300009 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300009 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300009/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300009 Building REAL300000300010 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300010' /scratch/stefan/7770550/working/building/REAL300000300010 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300010 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300010/0 /scratch/stefan/7770550/working/building/REAL300000300010 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/10 `/scratch/stefan/7770550/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)[N-][N-]C(=O)C1=CN=CC=N1) `REAL300000300010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300010 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)[N-][N-]C(=O)C1=CN=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 116, 71, 116, 116, 38, 12, 1, 12, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 1, 1, 1] 137 rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28]) total number of confs: 378 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300010 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)[N-][N-]C(=O)C1=CN=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 5, 11, 58, 108, 108, 137, 137, 137, 137, 137, 2, 2, 2, 1, 1, 137, 137, 137] 137 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 27, 28] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 328 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300010 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300010 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300010/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300010 Building REAL300000300011 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300011' /scratch/stefan/7770550/working/building/REAL300000300011 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300011 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300011/0 /scratch/stefan/7770550/working/building/REAL300000300011 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/11 `/scratch/stefan/7770550/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C([N+](=O)[O-])C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC=C1) `REAL300000300011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300011 none O=C([O-])C1=C([N+](=O)[O-])C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 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, 26, 26, 26, 26, 26, 26, 26, 24, 26, 26, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 26, 26, 26, 1, 1, 1, 26, 26, 26] 26 rigid atoms, others: [14, 16, 17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 28, 29, 30]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300011 none O=C([O-])C1=C([N+](=O)[O-])C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 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: [2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 13, 21, 21, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 1, 1, 1] 26 rigid atoms, others: [1, 3, 4, 5, 8, 9, 22, 23, 24, 28, 29, 30] set([0, 2, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300011 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300011 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300011/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300011 Building REAL300000300012 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300012' /scratch/stefan/7770550/working/building/REAL300000300012 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300012 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300012/0 /scratch/stefan/7770550/working/building/REAL300000300012 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/12 `/scratch/stefan/7770550/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(F)C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC=C1) `REAL300000300012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300012 none O=C([O-])C1=C(F)C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 164, 128, 80, 128, 128, 28, 12, 1, 12, 1, 1, 1, 1, 1, 1, 164, 164, 164, 1, 1, 1, 164, 164, 164] 164 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 26, 27, 28]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300012 none O=C([O-])C1=C(F)C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 15, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 7, 13, 61, 125, 125, 164, 164, 164, 164, 164, 1, 1, 1, 164, 164, 164, 1, 1, 1] 164 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20, 21, 22, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300012 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300012 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300012/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300012 Building REAL300000300013 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300013' /scratch/stefan/7770550/working/building/REAL300000300013 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300013 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300013/0 /scratch/stefan/7770550/working/building/REAL300000300013 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/13 `/scratch/stefan/7770550/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-]) `REAL300000300013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300013 none CC1=C(F)C=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 46, 43, 46, 46, 27, 7, 1, 7, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 48] 48 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300013 none CC1=C(F)C=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 19, 46, 46, 48, 48, 48, 48, 48, 1, 1, 1, 3, 3, 2, 2, 2, 1, 48, 48, 48, 1] 48 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300013 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300013 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300013/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300013 Building REAL300000300014 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300014' /scratch/stefan/7770550/working/building/REAL300000300014 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300014 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300014/0 /scratch/stefan/7770550/working/building/REAL300000300014 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/14 `/scratch/stefan/7770550/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC2=CC=CC=C21) `REAL300000300014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300014 none O=C([O-])C1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 41, 35, 41, 41, 19, 6, 1, 6, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 42, 42, 42, 42, 42] 42 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300014 none O=C([O-])C1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 2, 2, 2, 7, 19, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 1, 1, 1, 1, 1] 42 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300014 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300014 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300014/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300014 Building REAL300000300015 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300015' /scratch/stefan/7770550/working/building/REAL300000300015 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300015 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300015/0 /scratch/stefan/7770550/working/building/REAL300000300015 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/15 `/scratch/stefan/7770550/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=NC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=C1) `REAL300000300015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300015 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 109, 109, 109, 90, 57, 90, 90, 28, 10, 1, 10, 1, 1, 1, 1, 1, 1, 109, 109, 109, 1, 1, 1, 109] 109 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 27]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300015 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 72, 93, 93, 109, 109, 109, 109, 109, 1, 1, 1, 109, 109, 109, 1] 109 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300015 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300015 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300015/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300015 Building REAL300000300016 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300016' /scratch/stefan/7770550/working/building/REAL300000300016 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300016 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300016/0 /scratch/stefan/7770550/working/building/REAL300000300016 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/16 `/scratch/stefan/7770550/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-][N-]C(=O)C1=CN=CC=N1) `REAL300000300016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300016 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-][N-]C(=O)C1=CN=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 101, 65, 101, 101, 34, 11, 1, 11, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 1, 1, 1] 131 rigid atoms, others: [32, 16, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300016 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-][N-]C(=O)C1=CN=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 74, 119, 119, 131, 131, 131, 131, 131, 4, 4, 4, 1, 1, 1, 131, 131, 131] 131 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29] set([0, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300016 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300016 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300016/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300016 Building REAL300000300017 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300017' /scratch/stefan/7770550/working/building/REAL300000300017 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300017 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300017/0 /scratch/stefan/7770550/working/building/REAL300000300017 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/17 `/scratch/stefan/7770550/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=C(Cl)O1) `REAL300000300017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300017 none O=C([O-])C1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 16, 12, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 149, 149, 113, 79, 113, 113, 41, 12, 1, 12, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 1, 1, 1] 149 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22]) total number of confs: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300017 none O=C([O-])C1=CC(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 16, 12, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 7, 23, 75, 128, 128, 149, 149, 149, 149, 149, 1, 1, 1, 1, 149, 149, 149] 149 rigid atoms, others: [1, 3, 4, 5, 6, 19, 20, 21, 22] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300017 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300017 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300017/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300017 Building REAL300000300018 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300018' /scratch/stefan/7770550/working/building/REAL300000300018 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300018 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300018/0 /scratch/stefan/7770550/working/building/REAL300000300018 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/18 `/scratch/stefan/7770550/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C2=CC=C(S(=O)(=O)[N-][N-]C(=O)C3=CN=CC=N3)C=C2)CC1) `REAL300000300018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300018 none O=C([O-])C1(C2=CC=C(S(=O)(=O)[N-][N-]C(=O)C3=CN=CC=N3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 45, 170, 170, 194, 194, 194, 194, 194, 1, 1, 4, 4, 1, 1, 194, 194, 194, 1, 1, 4, 4, 4, 4] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 22, 25, 26, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 448 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300018 none O=C([O-])C1(C2=CC=C(S(=O)(=O)[N-][N-]C(=O)C3=CN=CC=N3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 4, 4, 4, 4, 5, 5, 5, 15, 51, 181, 181, 201, 201, 201, 201, 201, 4, 4, 1, 1, 4, 4, 201, 201, 201, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 3, 4, 33, 35, 23, 24] set([0, 2, 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]) total number of confs: 455 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: REAL300000300018 none O=C([O-])C1(C2=CC=C(S(=O)(=O)[N-][N-]C(=O)C3=CN=CC=N3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 194, 176, 194, 194, 176, 100, 176, 176, 37, 6, 1, 6, 1, 1, 1, 1, 1, 1, 194, 194, 201, 201, 194, 194, 1, 1, 1, 194, 194, 201, 201, 201, 201] 201 rigid atoms, others: [13, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 693 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300018 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300018 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300018/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300018 Building REAL300000300019 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300019' /scratch/stefan/7770550/working/building/REAL300000300019 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300019 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300019/0 /scratch/stefan/7770550/working/building/REAL300000300019 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/19 `/scratch/stefan/7770550/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC2=CC=C(S(=O)(=O)[N-][N-]C(=O)C3=CN=CC=N3)C=C2C1) `REAL300000300019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300019 none O=C([O-])C1CC2=CC=C(S(=O)(=O)[N-][N-]C(=O)C3=CN=CC=N3)C=C2C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 32, 37, 37, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 37, 37, 37] 37 rigid atoms, others: [32, 14, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300019 none O=C([O-])C1CC2=CC=C(S(=O)(=O)[N-][N-]C(=O)C3=CN=CC=N3)C=C2C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 35, 35, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 1, 1, 1] 37 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35] set([0, 32, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300019 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300019 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300019/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300019 Building REAL300000300020 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300020' /scratch/stefan/7770550/working/building/REAL300000300020 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300020 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300020/0 /scratch/stefan/7770550/working/building/REAL300000300020 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/20 `/scratch/stefan/7770550/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C(C(=O)[O-])O1) `REAL300000300020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300020 none CCC1=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 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, 193, 193, 144, 75, 144, 144, 35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 201, 201, 201, 201, 201, 1, 1, 1, 193] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300020 none CCC1=C(S(=O)(=O)[N-][N-]C(=O)C2=CN=CC=N2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 7, 7, 7, 21, 84, 160, 160, 193, 193, 193, 193, 193, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 193, 193, 193, 1] 201 rigid atoms, others: [1, 2, 3, 4, 17, 18, 19, 20, 21, 22, 31] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300020 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300020 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300020/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300020 Building REAL300000300021 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300021' /scratch/stefan/7770550/working/building/REAL300000300021 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300021 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300021/0 /scratch/stefan/7770550/working/building/REAL300000300021 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/21 `/scratch/stefan/7770550/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)C=C1) `REAL300000300021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300021 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 10, 19, 19, 19, 19, 15, 15, 15, 15, 7, 1, 1, 1, 1, 19, 19, 15, 15] 68 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300021 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 48, 68, 68, 68, 68, 1, 1, 1, 1, 5, 15, 15, 15, 15, 68, 68, 1, 1] 68 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 23, 24, 25, 26] set([0, 32, 2, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300021 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300021/1 /scratch/stefan/7770550/working/building/REAL300000300021 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/22 `/scratch/stefan/7770550/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)C=C1) `REAL300000300021.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300021 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 16, 16, 16, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 16, 16, 16, 16, 1, 1, 1, 1, 23, 23, 16, 16] 100 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300021 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 9, 16, 16, 16, 64, 100, 100, 100, 100, 1, 1, 1, 1, 16, 16, 16, 16, 100, 100, 1, 1] 100 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 33, 23, 24, 25, 26] set([0, 32, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300021 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300021 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300021/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300021/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300021 Building REAL300000300022 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300022' /scratch/stefan/7770550/working/building/REAL300000300022 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300022 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300022/0 /scratch/stefan/7770550/working/building/REAL300000300022 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/23 `/scratch/stefan/7770550/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=C1) `REAL300000300022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300022 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 9, 27, 27, 28, 27, 33, 33, 33, 33, 1, 1, 1, 1, 28, 28, 33] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300022 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 33, 33, 17, 33, 33, 33, 127, 201, 201, 201, 201, 1, 1, 1, 1, 33, 33, 33, 33, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27] set([32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300022 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300022/1 /scratch/stefan/7770550/working/building/REAL300000300022 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/24 `/scratch/stefan/7770550/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)=C1) `REAL300000300022.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300022 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 25, 24, 29, 29, 29, 29, 7, 1, 1, 1, 1, 24, 24, 29] 134 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300022 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 17, 29, 29, 29, 97, 134, 134, 134, 134, 1, 1, 1, 1, 9, 29, 29, 29, 29, 134, 134, 1] 134 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300022 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300022 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300022/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300022/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300022 Building REAL300000300023 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300023' /scratch/stefan/7770550/working/building/REAL300000300023 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300023 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300023/0 /scratch/stefan/7770550/working/building/REAL300000300023 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/25 `/scratch/stefan/7770550/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=C1) `REAL300000300023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300023 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 63, 63, 1, 1, 1, 1, 25, 25, 63] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 193 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300023 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 63, 63, 45, 63, 63, 63, 137, 201, 201, 201, 201, 1, 1, 63, 63, 63, 63, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300023 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300023 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300023/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300023 Building REAL300000300024 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300024' /scratch/stefan/7770550/working/building/REAL300000300024 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300024 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300024/0 /scratch/stefan/7770550/working/building/REAL300000300024 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/26 `/scratch/stefan/7770550/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)C=C1C(=O)[O-]) `REAL300000300024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300024 none CN1C=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 22, 22, 34] 198 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300024 none CN1C=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 34, 34, 17, 34, 34, 34, 124, 198, 198, 198, 198, 1, 1, 1, 1, 1, 2, 2, 2, 1, 34, 34, 34, 34, 198, 198, 1] 198 rigid atoms, others: [0, 1, 2, 3, 4, 35, 20, 21, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 627 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300024 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300024/1 /scratch/stefan/7770550/working/building/REAL300000300024 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/27 `/scratch/stefan/7770550/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)C=C1C(=O)[O-]) `REAL300000300024.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300024 none CN1C=C(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 1, 1, 1, 1, 25, 25, 29] 168 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300024 none CN1C=C(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 17, 29, 29, 29, 113, 168, 168, 168, 168, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 29, 29, 29, 29, 168, 168, 1] 168 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24, 36, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 551 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300024 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300024 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300024/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300024/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300024 Building REAL300000300025 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300025' /scratch/stefan/7770550/working/building/REAL300000300025 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300025 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300025/0 /scratch/stefan/7770550/working/building/REAL300000300025 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/28 `/scratch/stefan/7770550/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=CS1) `REAL300000300025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300025 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 24, 23, 35, 35, 35, 1, 1, 1, 1, 24, 24, 35] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31]) total number of confs: 169 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300025 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 2, 2, 2, 9, 35, 35, 17, 35, 35, 35, 127, 201, 201, 201, 201, 1, 1, 1, 35, 35, 35, 35, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 22, 23, 24, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30]) total number of confs: 636 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300025 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300025/1 /scratch/stefan/7770550/working/building/REAL300000300025 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/29 `/scratch/stefan/7770550/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)=CS1) `REAL300000300025.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300025 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 9, 25, 25, 26, 25, 29, 29, 29, 7, 1, 1, 1, 1, 26, 26, 29] 172 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300025 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=CC=C2SCC(F)(F)F)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 14, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 17, 29, 29, 29, 114, 172, 172, 172, 172, 1, 1, 1, 9, 29, 29, 29, 29, 172, 172, 1] 172 rigid atoms, others: [32, 1, 3, 4, 5, 6, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300025 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300025 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300025/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300025/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300025 Building REAL300000300026 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300026' /scratch/stefan/7770550/working/building/REAL300000300026 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300026 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300026/0 /scratch/stefan/7770550/working/building/REAL300000300026 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/30 `/scratch/stefan/7770550/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)C=C(C(=O)[O-])O1) `REAL300000300026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300026 none CC1=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 21, 21, 33] 114 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300026 none CC1=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 17, 33, 33, 25, 33, 33, 33, 74, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 2, 2, 2, 33, 33, 33, 33, 114, 114, 1] 114 rigid atoms, others: [0, 1, 2, 3, 34, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300026 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300026 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300026/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300026 Building REAL300000300027 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300027' /scratch/stefan/7770550/working/building/REAL300000300027 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300027 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300027/0 /scratch/stefan/7770550/working/building/REAL300000300027 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/31 `/scratch/stefan/7770550/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)S1) `REAL300000300027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300027 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 60, 60, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 23, 60, 60, 60, 1, 1, 1, 1, 23, 23] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300027 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 25, 60, 60, 44, 60, 60, 60, 143, 201, 201, 201, 201, 1, 1, 1, 60, 60, 60, 60, 201, 201] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 605 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300027 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300027 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300027/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300027 Building REAL300000300028 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300028' /scratch/stefan/7770550/working/building/REAL300000300028 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300028 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300028/0 /scratch/stefan/7770550/working/building/REAL300000300028 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/32 `/scratch/stefan/7770550/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=C1) `REAL300000300028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300028 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 71, 71, 71, 1, 1, 1, 1, 23, 23, 71] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300028 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=CC=C2SCC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 71, 71, 45, 71, 71, 71, 138, 201, 201, 201, 201, 1, 1, 1, 71, 71, 71, 71, 201, 201, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 33, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32]) total number of confs: 682 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300028 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300028 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300028/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300028 Building REAL300000300029 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300029' /scratch/stefan/7770550/working/building/REAL300000300029 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300029 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300029/0 /scratch/stefan/7770550/working/building/REAL300000300029 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/33 `/scratch/stefan/7770550/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1F) `REAL300000300029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300029 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 25, 45, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 49, 1, 1, 25, 25, 25, 25, 25, 6, 1, 1, 9, 49, 49, 49, 49, 49, 1, 1, 25, 25] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300029 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 18, 25, 94, 94, 94, 201, 201, 25, 25, 1, 1, 1, 1, 1, 9, 25, 25, 94, 201, 201, 201, 201, 201, 25, 25, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 22, 23, 24, 25, 26, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300029 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 148, 86, 149, 149, 39, 14, 49, 49, 13, 13, 1, 13, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 83, 49, 49, 13, 1, 1, 1, 1, 1, 49, 49, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 723 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300029 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300029 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300029/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300029 Building REAL300000300030 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300030' /scratch/stefan/7770550/working/building/REAL300000300030 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300030 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300030/0 /scratch/stefan/7770550/working/building/REAL300000300030 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/34 `/scratch/stefan/7770550/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1) `REAL300000300030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300030 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 6, 11, 11, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 1, 1, 11, 11, 11, 11, 6, 1, 1, 9, 37, 37, 37, 37, 37, 1, 1, 11, 11] 61 rigid atoms, others: [36, 37, 10, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300030 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 5, 11, 11, 5, 5, 39, 40, 40, 61, 61, 11, 11, 1, 1, 1, 1, 5, 11, 11, 39, 61, 61, 61, 61, 61, 11, 11, 1, 1] 61 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300030 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 49, 61, 61, 28, 26, 37, 37, 10, 10, 1, 10, 1, 1, 1, 37, 37, 61, 61, 61, 61, 48, 37, 37, 10, 1, 1, 1, 1, 1, 37, 37, 61, 61] 61 rigid atoms, others: [32, 33, 34, 35, 16, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 228 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300030 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300030 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300030/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300030 Building REAL300000300031 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300031' /scratch/stefan/7770550/working/building/REAL300000300031 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300031 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300031/0 /scratch/stefan/7770550/working/building/REAL300000300031 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/35 `/scratch/stefan/7770550/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300031 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 41, 1, 1, 24, 24, 24, 24, 6, 1, 1, 9, 41, 41, 41, 41, 41, 1, 1, 24] 126 rigid atoms, others: [37, 38, 11, 12, 13, 14, 15, 16, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300031 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 24, 24, 17, 24, 85, 85, 85, 126, 126, 24, 24, 1, 1, 1, 1, 9, 24, 24, 85, 126, 126, 126, 126, 126, 24, 24, 1] 126 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300031 none O=C([O-])C1=CC=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 126, 126, 126, 88, 55, 88, 88, 32, 13, 41, 41, 13, 13, 1, 13, 1, 1, 1, 41, 41, 126, 126, 126, 126, 54, 41, 41, 13, 1, 1, 1, 1, 1, 41, 41, 126] 126 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 446 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300031 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300031/1 /scratch/stefan/7770550/working/building/REAL300000300031 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/36 `/scratch/stefan/7770550/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300031.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300031 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 1, 1, 27, 27, 27, 27, 1, 1, 9, 37, 37, 37, 37, 37, 1, 1, 27] 129 rigid atoms, others: [36, 37, 11, 12, 13, 14, 15, 16, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300031 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 16, 27, 90, 90, 90, 129, 129, 27, 27, 1, 1, 1, 1, 27, 27, 90, 129, 129, 129, 129, 129, 27, 27, 1] 129 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300031 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 129, 129, 129, 129, 94, 58, 94, 92, 28, 12, 37, 37, 11, 11, 1, 11, 1, 1, 1, 37, 37, 129, 129, 129, 129, 37, 37, 11, 1, 1, 1, 1, 1, 37, 37, 129] 129 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 435 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300031 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300031 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300031/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300031/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300031 Building REAL300000300032 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300032' /scratch/stefan/7770550/working/building/REAL300000300032 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300032 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300032/0 /scratch/stefan/7770550/working/building/REAL300000300032 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/37 `/scratch/stefan/7770550/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300032 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 43, 1, 1, 79, 79, 79, 49, 49, 49, 1, 1, 9, 43, 43, 43, 43, 43, 1, 1] 201 rigid atoms, others: [33, 34, 41, 42, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300032 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 7, 7, 7, 23, 49, 49, 34, 49, 128, 128, 128, 201, 201, 49, 49, 4, 4, 4, 1, 1, 1, 49, 49, 128, 201, 201, 201, 201, 201, 49, 49] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 658 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300032 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 200, 200, 200, 200, 200, 200, 200, 116, 67, 117, 117, 31, 13, 43, 43, 13, 13, 1, 13, 1, 1, 1, 43, 43, 201, 201, 201, 201, 200, 200, 43, 43, 13, 1, 1, 1, 1, 1, 43, 43] 201 rigid atoms, others: [36, 37, 38, 39, 40, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 577 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300032 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300032/1 /scratch/stefan/7770550/working/building/REAL300000300032 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/38 `/scratch/stefan/7770550/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300032.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300032 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 47, 47, 47, 47, 47, 47, 47, 47, 47, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 49, 1, 1, 64, 64, 64, 47, 47, 47, 6, 1, 1, 9, 49, 49, 49, 49, 49, 1, 1] 201 rigid atoms, others: [34, 35, 42, 43, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300032 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 47, 47, 37, 47, 142, 142, 142, 201, 201, 47, 47, 4, 4, 4, 1, 1, 1, 23, 47, 47, 142, 201, 201, 201, 201, 201, 47, 47] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 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: REAL300000300032 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 151, 93, 151, 150, 37, 13, 49, 49, 13, 13, 1, 13, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 201, 90, 49, 49, 13, 1, 1, 1, 1, 1, 49, 49] 201 rigid atoms, others: [37, 38, 39, 40, 41, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 710 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300032 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300032 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300032/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300032/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300032 Building REAL300000300033 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300033' /scratch/stefan/7770550/working/building/REAL300000300033 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300033 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300033/0 /scratch/stefan/7770550/working/building/REAL300000300033 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/39 `/scratch/stefan/7770550/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1) `REAL300000300033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300033 none O=C([O-])C=CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 33, 85, 33, 17, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 51, 51, 1, 1, 17, 17, 33, 33, 17, 17, 4, 1, 1, 9, 51, 51, 51, 51, 51, 1, 1, 17, 17] 201 rigid atoms, others: [32, 33, 40, 41, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 389 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300033 none O=C([O-])C=CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 12, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 9, 76, 76, 76, 201, 201, 17, 17, 1, 1, 3, 3, 1, 1, 9, 17, 17, 76, 201, 201, 201, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 43, 25, 26, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 624 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: REAL300000300033 none O=C([O-])C=CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 137, 81, 137, 137, 37, 37, 51, 51, 12, 12, 1, 12, 1, 1, 1, 51, 51, 201, 201, 201, 201, 201, 201, 79, 51, 51, 12, 1, 1, 1, 1, 1, 51, 51, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43]) total number of confs: 654 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300033 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300033/1 /scratch/stefan/7770550/working/building/REAL300000300033 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/40 `/scratch/stefan/7770550/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1) `REAL300000300033.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300033 none O=C([O-])C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 94, 34, 18, 18, 18, 18, 10, 4, 10, 10, 1, 1, 1, 1, 1, 1, 9, 9, 9, 47, 47, 1, 1, 18, 18, 34, 34, 18, 18, 1, 1, 9, 47, 47, 47, 47, 47, 1, 1, 18, 18] 201 rigid atoms, others: [32, 39, 40, 12, 13, 14, 15, 16, 17, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 398 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300033 none O=C([O-])C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 18, 18, 13, 13, 77, 77, 77, 201, 201, 18, 18, 1, 1, 3, 3, 1, 1, 18, 18, 77, 201, 201, 201, 201, 201, 18, 18, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 41, 25, 26, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 608 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: REAL300000300033 none O=C([O-])C=CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 142, 83, 142, 142, 39, 28, 47, 47, 13, 13, 1, 13, 1, 1, 1, 47, 47, 201, 201, 201, 201, 201, 201, 47, 47, 13, 1, 1, 1, 1, 1, 47, 47, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42]) total number of confs: 620 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300033 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300033 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300033/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300033/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300033 Building REAL300000300034 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300034' /scratch/stefan/7770550/working/building/REAL300000300034 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300034 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300034/0 /scratch/stefan/7770550/working/building/REAL300000300034 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/41 `/scratch/stefan/7770550/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300034 none CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 58, 58, 1, 1, 25, 25, 25, 46, 46, 25, 25, 25, 25, 25, 6, 1, 1, 9, 58, 58, 58, 58, 58, 1, 1, 25] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 40, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300034 none CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 18, 25, 101, 101, 101, 201, 201, 25, 25, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 9, 25, 25, 101, 201, 201, 201, 201, 201, 25, 25, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 21, 22, 23, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300034 none CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 154, 82, 153, 157, 42, 13, 58, 58, 13, 13, 1, 13, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 58, 58, 13, 1, 1, 1, 1, 1, 58, 58, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 762 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300034 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300034 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300034/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300034 Building REAL300000300035 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300035' /scratch/stefan/7770550/working/building/REAL300000300035 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300035 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300035/0 /scratch/stefan/7770550/working/building/REAL300000300035 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/42 `/scratch/stefan/7770550/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300035 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 1, 1, 25, 25, 25, 1, 1, 9, 37, 37, 37, 37, 37, 1, 1, 25] 107 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300035 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 25, 25, 11, 11, 59, 69, 75, 107, 107, 25, 25, 1, 1, 1, 25, 25, 59, 107, 107, 107, 107, 107, 25, 25, 1] 107 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 38, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300035 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 107, 95, 65, 95, 95, 35, 28, 37, 37, 11, 11, 1, 11, 1, 1, 1, 37, 37, 107, 107, 107, 37, 37, 11, 1, 1, 1, 1, 1, 37, 37, 107] 107 rigid atoms, others: [32, 33, 34, 35, 18, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 334 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300035 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300035/1 /scratch/stefan/7770550/working/building/REAL300000300035 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/43 `/scratch/stefan/7770550/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300035.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300035 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 1, 1, 25, 25, 25, 6, 1, 1, 9, 37, 37, 37, 37, 37, 1, 1, 25] 112 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300035 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 25, 25, 12, 11, 62, 67, 79, 112, 112, 25, 25, 1, 1, 1, 11, 25, 25, 62, 112, 112, 112, 112, 112, 25, 25, 1] 112 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300035 none O=C([O-])C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 112, 112, 112, 112, 104, 66, 104, 104, 33, 29, 37, 37, 11, 11, 1, 11, 1, 1, 1, 37, 37, 112, 112, 112, 66, 37, 37, 11, 1, 1, 1, 1, 1, 37, 37, 112] 112 rigid atoms, others: [32, 33, 34, 35, 36, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 399 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300035 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300035 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300035/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300035/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300035 Building REAL300000300036 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300036' /scratch/stefan/7770550/working/building/REAL300000300036 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300036 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300036/0 /scratch/stefan/7770550/working/building/REAL300000300036 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/44 `/scratch/stefan/7770550/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1Cl) `REAL300000300036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300036 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [35, 25, 35, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 47, 47, 1, 1, 25, 25, 25, 25, 25, 6, 1, 1, 9, 47, 47, 47, 47, 47, 1, 1, 25, 25] 147 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300036 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 18, 25, 99, 99, 99, 147, 147, 25, 25, 1, 1, 1, 1, 1, 9, 25, 25, 99, 147, 147, 147, 147, 147, 25, 25, 1, 1] 147 rigid atoms, others: [1, 3, 4, 5, 6, 39, 22, 23, 24, 25, 26, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300036 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 147, 110, 73, 110, 111, 33, 13, 47, 47, 13, 13, 1, 13, 1, 1, 1, 47, 47, 147, 147, 147, 147, 147, 70, 47, 47, 13, 1, 1, 1, 1, 1, 47, 47, 147, 147] 147 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 541 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300036 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300036/1 /scratch/stefan/7770550/working/building/REAL300000300036 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/45 `/scratch/stefan/7770550/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1Cl) `REAL300000300036.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300036 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 29, 43, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 44, 44, 1, 1, 29, 29, 29, 29, 29, 1, 1, 9, 44, 44, 44, 44, 44, 1, 1, 29, 29] 153 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300036 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 17, 29, 107, 107, 107, 153, 153, 29, 29, 1, 1, 1, 1, 1, 29, 29, 107, 153, 153, 153, 153, 153, 29, 29, 1, 1] 153 rigid atoms, others: [1, 3, 4, 5, 6, 22, 23, 24, 25, 26, 38, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300036 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 153, 121, 71, 120, 121, 30, 13, 44, 44, 11, 11, 1, 11, 1, 1, 1, 44, 44, 153, 153, 153, 153, 153, 44, 44, 11, 1, 1, 1, 1, 1, 44, 44, 153, 153] 153 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 518 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300036 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300036 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300036/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300036/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300036 Building REAL300000300037 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300037' /scratch/stefan/7770550/working/building/REAL300000300037 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300037 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300037/0 /scratch/stefan/7770550/working/building/REAL300000300037 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/46 `/scratch/stefan/7770550/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1C) `REAL300000300037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300037 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 41, 1, 1, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 9, 41, 41, 41, 41, 41, 1, 1, 17, 17, 17] 81 rigid atoms, others: [33, 34, 41, 42, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300037 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 5, 17, 17, 13, 17, 71, 71, 71, 81, 81, 17, 17, 1, 1, 2, 2, 2, 1, 1, 5, 17, 17, 71, 81, 81, 81, 81, 81, 17, 17, 2, 2, 2] 81 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 25, 26, 30, 31] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300037 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 81, 81, 66, 81, 81, 30, 11, 41, 41, 11, 11, 1, 11, 1, 1, 1, 41, 41, 81, 81, 81, 81, 81, 81, 81, 64, 41, 41, 11, 1, 1, 1, 1, 1, 41, 41, 81, 81, 81] 81 rigid atoms, others: [36, 37, 38, 39, 40, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45]) total number of confs: 330 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300037 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300037 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300037/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300037 Building REAL300000300038 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300038' /scratch/stefan/7770550/working/building/REAL300000300038 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300038 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300038/0 /scratch/stefan/7770550/working/building/REAL300000300038 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/47 `/scratch/stefan/7770550/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300038 none O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 57, 57, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 56, 56, 1, 1, 57, 57, 57, 1, 1, 9, 56, 56, 56, 56, 56, 1, 1, 57] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300038 none O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 57, 57, 25, 25, 136, 142, 144, 201, 201, 57, 57, 1, 1, 1, 57, 57, 136, 201, 201, 201, 201, 201, 57, 57, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 38, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 698 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300038 none O=C([O-])C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 157, 97, 156, 157, 53, 41, 56, 56, 13, 13, 1, 13, 1, 1, 1, 56, 56, 201, 201, 201, 56, 56, 13, 1, 1, 1, 1, 1, 56, 56, 201] 201 rigid atoms, others: [32, 33, 34, 35, 18, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 588 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300038 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300038 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300038/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300038 Building REAL300000300039 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300039' /scratch/stefan/7770550/working/building/REAL300000300039 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300039 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300039/0 /scratch/stefan/7770550/working/building/REAL300000300039 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/48 `/scratch/stefan/7770550/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1) `REAL300000300039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300039 none O=C([O-])CCC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 46, 75, 25, 9, 9, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 8, 8, 8, 42, 42, 1, 1, 17, 17, 46, 46, 25, 25, 17, 17, 4, 1, 1, 8, 42, 42, 42, 42, 42, 1, 1, 17, 17] 201 rigid atoms, others: [34, 35, 42, 43, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300039 none O=C([O-])CCC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 9, 62, 63, 64, 133, 133, 17, 17, 1, 1, 7, 7, 3, 3, 1, 1, 9, 17, 17, 62, 133, 133, 133, 133, 133, 17, 17, 1, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 44, 45, 25, 26, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 482 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300039 none O=C([O-])CCC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 150, 94, 93, 133, 133, 92, 67, 93, 91, 34, 34, 42, 42, 12, 12, 1, 12, 1, 1, 1, 42, 42, 135, 135, 201, 201, 150, 150, 133, 133, 66, 42, 42, 12, 1, 1, 1, 1, 1, 42, 42, 135, 135] 201 rigid atoms, others: [37, 38, 39, 40, 41, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45]) total number of confs: 1063 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300039 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300039/1 /scratch/stefan/7770550/working/building/REAL300000300039 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/49 `/scratch/stefan/7770550/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1) `REAL300000300039.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300039 none O=C([O-])CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [47, 27, 47, 27, 9, 9, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 40, 40, 1, 1, 17, 17, 27, 27, 27, 27, 17, 17, 1, 1, 9, 40, 40, 40, 40, 40, 1, 1, 17, 17] 118 rigid atoms, others: [33, 34, 41, 42, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300039 none O=C([O-])CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [10, 3, 10, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 13, 13, 59, 59, 59, 114, 114, 17, 17, 1, 1, 3, 3, 3, 3, 1, 1, 17, 17, 59, 114, 114, 114, 114, 114, 17, 17, 1, 1] 118 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 43, 44, 25, 26, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300039 none O=C([O-])CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 75, 75, 114, 114, 75, 61, 75, 75, 33, 27, 40, 40, 13, 13, 1, 13, 1, 1, 1, 40, 40, 114, 114, 118, 118, 118, 118, 114, 114, 40, 40, 13, 1, 1, 1, 1, 1, 40, 40, 114, 114] 118 rigid atoms, others: [36, 37, 38, 39, 40, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44]) total number of confs: 667 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300039 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300039 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300039/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300039/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300039 Building REAL300000300040 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300040' /scratch/stefan/7770550/working/building/REAL300000300040 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300040 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300040/0 /scratch/stefan/7770550/working/building/REAL300000300040 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/50 `/scratch/stefan/7770550/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300040 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 56, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 9, 9, 9, 48, 48, 1, 1, 56, 56, 1, 1, 9, 48, 48, 48, 48, 48, 1, 1, 56] 201 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300040 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 56, 56, 25, 25, 116, 120, 122, 201, 201, 56, 56, 1, 1, 56, 56, 115, 201, 201, 201, 201, 201, 56, 56, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 23, 24] set([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]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300040 none O=C([O-])C1=CSC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 138, 84, 137, 138, 44, 37, 48, 48, 11, 11, 1, 11, 1, 1, 1, 48, 48, 201, 201, 48, 48, 11, 1, 1, 1, 1, 1, 48, 48, 201] 201 rigid atoms, others: [32, 16, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35]) total number of confs: 551 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300040 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300040 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300040/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300040 Building REAL300000300041 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300041' /scratch/stefan/7770550/working/building/REAL300000300041 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300041 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300041/0 /scratch/stefan/7770550/working/building/REAL300000300041 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/51 `/scratch/stefan/7770550/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300041 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 51, 51, 1, 1, 29, 29, 29, 29, 29, 29, 6, 1, 1, 9, 51, 51, 51, 51, 51, 1, 1] 143 rigid atoms, others: [33, 34, 41, 42, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300041 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 29, 29, 22, 29, 113, 113, 113, 143, 143, 29, 29, 2, 2, 2, 1, 1, 1, 13, 29, 29, 113, 143, 143, 143, 143, 143, 29, 29] 143 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300041 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 143, 143, 143, 143, 143, 143, 135, 89, 135, 137, 39, 13, 51, 51, 13, 13, 1, 13, 1, 1, 1, 51, 51, 143, 143, 143, 143, 143, 143, 89, 51, 51, 13, 1, 1, 1, 1, 1, 51, 51] 143 rigid atoms, others: [36, 37, 38, 39, 40, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 547 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300041 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300041 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300041/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300041 Building REAL300000300042 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300042' /scratch/stefan/7770550/working/building/REAL300000300042 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300042 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300042/0 /scratch/stefan/7770550/working/building/REAL300000300042 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/52 `/scratch/stefan/7770550/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1) `REAL300000300042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300042 none O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 73, 109, 31, 13, 13, 13, 13, 7, 4, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 39, 1, 1, 13, 13, 73, 73, 13, 13, 4, 1, 1, 7, 39, 39, 39, 39, 39, 1, 1, 13, 13] 201 rigid atoms, others: [32, 33, 40, 41, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 475 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300042 none O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 13, 26, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 13, 13, 9, 9, 36, 36, 36, 110, 110, 13, 13, 1, 1, 13, 13, 1, 1, 9, 13, 13, 36, 110, 110, 110, 110, 110, 13, 13, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 42, 43, 25, 26, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 399 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300042 none O=C([O-])COC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 110, 110, 110, 110, 74, 60, 74, 74, 36, 35, 39, 39, 13, 13, 1, 13, 1, 1, 1, 39, 39, 110, 110, 201, 201, 110, 110, 60, 39, 39, 13, 1, 1, 1, 1, 1, 39, 39, 110, 110] 201 rigid atoms, others: [35, 36, 37, 38, 39, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43]) total number of confs: 643 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300042 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300042 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300042/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300042 Building REAL300000300043 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300043' /scratch/stefan/7770550/working/building/REAL300000300043 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300043 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300043/0 /scratch/stefan/7770550/working/building/REAL300000300043 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/53 `/scratch/stefan/7770550/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300043 none CN1C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 29, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 54, 54, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 1, 1, 9, 54, 54, 54, 54, 54, 1, 1, 29] 151 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 18, 19, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300043 none CN1C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 3, 3, 9, 29, 29, 22, 29, 103, 103, 103, 151, 151, 29, 29, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 29, 29, 103, 151, 151, 151, 151, 151, 29, 29, 1] 151 rigid atoms, others: [0, 1, 2, 3, 4, 40, 20, 21, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 483 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300043 none CN1C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 109, 75, 109, 108, 37, 16, 54, 54, 13, 13, 1, 13, 1, 1, 1, 54, 54, 151, 151, 151, 151, 151, 151, 151, 151, 151, 75, 54, 54, 13, 1, 1, 1, 1, 1, 54, 54, 151] 151 rigid atoms, others: [33, 34, 35, 36, 37, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 542 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300043 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300043/1 /scratch/stefan/7770550/working/building/REAL300000300043 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/54 `/scratch/stefan/7770550/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300043.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300043 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 53, 53, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 9, 53, 53, 53, 53, 53, 1, 1, 31] 160 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300043 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 31, 31, 17, 31, 111, 111, 111, 160, 160, 31, 31, 1, 1, 1, 1, 1, 2, 2, 2, 1, 31, 31, 111, 160, 160, 160, 160, 160, 31, 31, 1] 160 rigid atoms, others: [0, 1, 2, 3, 4, 39, 20, 21, 22, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300043 none CN1C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 116, 76, 116, 116, 36, 13, 53, 53, 13, 13, 1, 13, 1, 1, 1, 53, 53, 160, 160, 160, 160, 160, 160, 160, 160, 160, 53, 53, 13, 1, 1, 1, 1, 1, 53, 53, 160] 160 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 533 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300043 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300043 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300043/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300043/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300043 Building REAL300000300044 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300044' /scratch/stefan/7770550/working/building/REAL300000300044 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300044 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300044/0 /scratch/stefan/7770550/working/building/REAL300000300044 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/55 `/scratch/stefan/7770550/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300044 none CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 272 conformations in input total number of sets (complete confs): 272 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 53, 53, 1, 1, 29, 29, 29, 29, 58, 29, 6, 1, 1, 9, 53, 53, 53, 53, 53, 1, 1] 272 rigid atoms, others: [34, 35, 42, 43, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300044 none CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 272 conformations in input total number of sets (complete confs): 272 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 13, 29, 29, 23, 29, 116, 116, 116, 136, 136, 29, 29, 2, 2, 2, 1, 2, 1, 13, 29, 29, 116, 136, 136, 136, 136, 136, 29, 29] 272 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 9, 10, 11, 30] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300044 none CC1=CC(O)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 272 conformations in input total number of sets (complete confs): 272 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 124, 86, 124, 124, 37, 16, 53, 53, 13, 13, 1, 13, 1, 1, 1, 53, 53, 136, 136, 136, 136, 272, 136, 86, 53, 53, 13, 1, 1, 1, 1, 1, 53, 53] 272 rigid atoms, others: [37, 38, 39, 40, 41, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 794 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300044 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300044 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300044/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300044 Building REAL300000300045 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300045' /scratch/stefan/7770550/working/building/REAL300000300045 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300045 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300045/0 /scratch/stefan/7770550/working/building/REAL300000300045 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/56 `/scratch/stefan/7770550/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300045 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 63, 63, 55, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 9, 9, 9, 55, 55, 1, 1, 55, 55, 55, 55, 1, 1, 9, 55, 55, 55, 55, 55, 1, 1, 55] 201 rigid atoms, others: [36, 37, 11, 12, 13, 14, 15, 16, 22, 23, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300045 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 25, 55, 55, 39, 55, 131, 131, 131, 201, 201, 55, 55, 1, 2, 2, 2, 55, 55, 131, 201, 201, 201, 201, 201, 55, 55, 1] 201 rigid atoms, others: [0, 1, 2, 3, 38, 6, 7, 8, 24] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300045 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 154, 90, 153, 154, 36, 12, 55, 55, 12, 12, 1, 12, 1, 1, 1, 55, 55, 201, 201, 201, 201, 55, 55, 12, 1, 1, 1, 1, 1, 55, 55, 201] 201 rigid atoms, others: [32, 33, 34, 35, 17, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 669 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300045 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300045 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300045/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300045 Building REAL300000300046 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300046' /scratch/stefan/7770550/working/building/REAL300000300046 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300046 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300046/0 /scratch/stefan/7770550/working/building/REAL300000300046 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/57 `/scratch/stefan/7770550/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300046 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 44, 44, 1, 1, 17, 17, 17, 31, 31, 17, 17, 17, 17, 17, 17, 17, 6, 1, 1, 9, 44, 44, 44, 44, 44, 1, 1, 17] 137 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 44, 43, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300046 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 13, 17, 77, 77, 77, 137, 137, 17, 17, 1, 1, 1, 3, 3, 2, 2, 2, 1, 2, 2, 2, 5, 17, 17, 77, 137, 137, 137, 137, 137, 17, 17, 1] 137 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 45, 22, 23, 24, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300046 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 137, 137, 85, 137, 137, 33, 12, 44, 44, 11, 11, 1, 11, 1, 1, 1, 44, 44, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 83, 44, 44, 11, 1, 1, 1, 1, 1, 44, 44, 137] 137 rigid atoms, others: [38, 39, 40, 41, 42, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 557 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300046 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300046 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300046/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300046 Building REAL300000300047 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300047' /scratch/stefan/7770550/working/building/REAL300000300047 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300047 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300047/0 /scratch/stefan/7770550/working/building/REAL300000300047 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/58 `/scratch/stefan/7770550/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CS1) `REAL300000300047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300047 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 45, 1, 1, 27, 27, 27, 1, 1, 9, 45, 45, 45, 45, 45, 1, 1, 27] 152 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300047 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 16, 18, 100, 100, 100, 152, 152, 27, 27, 1, 1, 1, 27, 27, 100, 152, 152, 152, 152, 152, 27, 27, 1] 152 rigid atoms, others: [1, 3, 4, 5, 6, 35, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 485 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300047 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 152, 152, 113, 67, 112, 113, 36, 28, 45, 45, 13, 13, 1, 13, 1, 1, 1, 45, 45, 152, 152, 152, 45, 45, 13, 1, 1, 1, 1, 1, 45, 45, 152] 152 rigid atoms, others: [32, 15, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35]) total number of confs: 513 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300047 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300047/1 /scratch/stefan/7770550/working/building/REAL300000300047 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/59 `/scratch/stefan/7770550/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CS1) `REAL300000300047.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300047 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 14, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 44, 44, 1, 1, 26, 26, 26, 6, 1, 1, 9, 44, 44, 44, 44, 44, 1, 1, 26] 146 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300047 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 14, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 3, 3, 3, 9, 26, 26, 19, 26, 94, 94, 94, 146, 146, 26, 26, 1, 1, 1, 9, 26, 26, 94, 146, 146, 146, 146, 146, 26, 26, 1] 146 rigid atoms, others: [1, 3, 4, 5, 6, 22, 23, 24, 36] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300047 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 14, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 146, 93, 60, 92, 93, 32, 13, 44, 44, 13, 13, 1, 13, 1, 1, 1, 44, 44, 146, 146, 146, 58, 44, 44, 13, 1, 1, 1, 1, 1, 44, 44, 146] 146 rigid atoms, others: [32, 33, 15, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36]) total number of confs: 499 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300047 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300047 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300047/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300047/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300047 Building REAL300000300048 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300048' /scratch/stefan/7770550/working/building/REAL300000300048 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300048 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300048/0 /scratch/stefan/7770550/working/building/REAL300000300048 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/60 `/scratch/stefan/7770550/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300048 none COC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 19, 19, 19, 19, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 34, 1, 1, 19, 19, 19, 31, 31, 35, 35, 35, 19, 19, 4, 1, 1, 9, 34, 34, 34, 34, 34, 1, 1, 19] 201 rigid atoms, others: [33, 34, 9, 10, 11, 12, 13, 14, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300048 none COC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 14, 19, 65, 65, 65, 136, 136, 19, 19, 1, 1, 1, 3, 3, 4, 4, 4, 1, 1, 9, 19, 19, 65, 136, 136, 136, 136, 136, 19, 19, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 22, 23, 24, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300048 none COC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 136, 136, 136, 136, 91, 49, 92, 92, 28, 9, 34, 34, 9, 9, 1, 9, 1, 1, 1, 34, 34, 136, 136, 136, 201, 201, 201, 201, 201, 136, 136, 48, 34, 34, 9, 1, 1, 1, 1, 1, 34, 34, 136] 201 rigid atoms, others: [36, 37, 38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43]) total number of confs: 864 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300048 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300048 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300048/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300048 Building REAL300000300049 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300049' /scratch/stefan/7770550/working/building/REAL300000300049 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300049 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300049/0 /scratch/stefan/7770550/working/building/REAL300000300049 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/61 `/scratch/stefan/7770550/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300049 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 28, 28, 28, 28, 28, 28, 28, 28, 28, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 61, 61, 1, 1, 67, 67, 67, 67, 67, 28, 28, 28, 6, 1, 1, 9, 61, 61, 61, 61, 61, 1, 1] 201 rigid atoms, others: [36, 37, 44, 45, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300049 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 5, 5, 5, 13, 28, 28, 23, 28, 106, 106, 106, 201, 201, 28, 28, 6, 6, 6, 5, 5, 1, 1, 1, 13, 28, 28, 106, 201, 201, 201, 201, 201, 28, 28] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 9, 10, 11, 34] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300049 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 200, 201, 163, 106, 163, 163, 40, 22, 61, 61, 13, 13, 1, 13, 1, 1, 1, 61, 61, 201, 201, 201, 201, 201, 201, 201, 200, 106, 61, 61, 13, 1, 1, 1, 1, 1, 61, 61] 201 rigid atoms, others: [39, 40, 41, 42, 43, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 734 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300049 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300049/1 /scratch/stefan/7770550/working/building/REAL300000300049 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/62 `/scratch/stefan/7770550/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300049.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300049 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 58, 58, 1, 1, 72, 72, 72, 72, 72, 37, 37, 37, 1, 1, 9, 58, 58, 58, 58, 58, 1, 1] 201 rigid atoms, others: [35, 36, 43, 44, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300049 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 37, 37, 26, 37, 113, 113, 113, 201, 201, 37, 37, 6, 6, 6, 6, 6, 1, 1, 1, 37, 37, 113, 201, 201, 201, 201, 201, 37, 37] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 34, 11] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300049 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 94, 164, 164, 39, 13, 58, 58, 13, 13, 1, 13, 1, 1, 1, 58, 58, 201, 201, 201, 201, 201, 201, 201, 201, 58, 58, 13, 1, 1, 1, 1, 1, 58, 58] 201 rigid atoms, others: [38, 39, 40, 41, 42, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44]) total number of confs: 675 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300049 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300049 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300049/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300049/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300049 Building REAL300000300050 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300050' /scratch/stefan/7770550/working/building/REAL300000300050 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300050 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300050/0 /scratch/stefan/7770550/working/building/REAL300000300050 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/63 `/scratch/stefan/7770550/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1) `REAL300000300050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300050 none CC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 9, 9, 9, 63, 63, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 9, 63, 63, 63, 63, 63, 1, 1, 46] 193 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300050 none CC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 23, 46, 46, 32, 46, 133, 133, 133, 193, 193, 46, 46, 1, 1, 1, 1, 1, 1, 2, 2, 2, 46, 46, 133, 193, 193, 193, 193, 193, 46, 46, 1] 193 rigid atoms, others: [0, 1, 2, 3, 38, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300050 none CC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 169, 114, 169, 167, 39, 13, 63, 63, 13, 13, 1, 13, 1, 1, 1, 63, 63, 193, 193, 193, 193, 193, 193, 193, 193, 193, 63, 63, 13, 1, 1, 1, 1, 1, 63, 63, 193] 193 rigid atoms, others: [32, 33, 34, 35, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 620 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300050 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300050/1 /scratch/stefan/7770550/working/building/REAL300000300050 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/64 `/scratch/stefan/7770550/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1) `REAL300000300050.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300050 none CC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 10, 10, 10, 53, 53, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 1, 1, 10, 53, 53, 53, 53, 53, 1, 1, 37] 182 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 17, 18, 38, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300050 none CC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 15, 37, 37, 28, 37, 128, 128, 128, 182, 182, 37, 37, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 37, 37, 128, 182, 182, 182, 182, 182, 37, 37, 1] 182 rigid atoms, others: [0, 1, 2, 3, 39, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300050 none CC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 158, 91, 158, 157, 33, 13, 53, 53, 13, 13, 1, 13, 1, 1, 1, 53, 53, 182, 182, 182, 182, 182, 182, 182, 182, 182, 87, 53, 53, 13, 1, 1, 1, 1, 1, 53, 53, 182] 182 rigid atoms, others: [32, 33, 34, 35, 36, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 677 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300050 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300050 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300050/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300050/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300050 Building REAL300000300051 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300051' /scratch/stefan/7770550/working/building/REAL300000300051 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300051 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300051/0 /scratch/stefan/7770550/working/building/REAL300000300051 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/65 `/scratch/stefan/7770550/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300051 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 67, 67, 44, 44, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 1, 1, 44, 44, 44, 44, 44, 88, 1, 1, 9, 50, 50, 50, 50, 50, 1, 1, 44] 402 rigid atoms, others: [32, 33, 40, 41, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300051 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 23, 44, 44, 32, 42, 123, 123, 123, 201, 201, 44, 44, 1, 2, 2, 2, 1, 2, 44, 44, 123, 201, 201, 201, 201, 201, 44, 44, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 42, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 639 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300051 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 134, 77, 134, 135, 38, 13, 50, 50, 13, 13, 1, 13, 1, 1, 1, 50, 50, 201, 201, 201, 201, 201, 402, 50, 50, 13, 1, 1, 1, 1, 1, 50, 50, 201] 402 rigid atoms, others: [35, 36, 37, 38, 39, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 1017 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300051 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300051/1 /scratch/stefan/7770550/working/building/REAL300000300051 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/66 `/scratch/stefan/7770550/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300051.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300051 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 334 conformations in input total number of sets (complete confs): 334 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 56, 56, 37, 37, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 46, 46, 1, 1, 37, 37, 37, 37, 37, 74, 6, 1, 1, 9, 46, 46, 46, 46, 46, 1, 1, 37] 334 rigid atoms, others: [33, 34, 41, 42, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300051 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 334 conformations in input total number of sets (complete confs): 334 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 19, 37, 37, 29, 37, 107, 107, 107, 167, 167, 37, 37, 1, 2, 2, 2, 1, 2, 19, 37, 37, 107, 167, 167, 167, 167, 167, 37, 37, 1] 334 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 43, 26, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300051 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 334 conformations in input total number of sets (complete confs): 334 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 167, 167, 167, 167, 167, 167, 167, 128, 72, 128, 128, 34, 13, 46, 46, 13, 13, 1, 13, 1, 1, 1, 46, 46, 167, 166, 166, 167, 167, 334, 71, 46, 46, 13, 1, 1, 1, 1, 1, 46, 46, 167] 334 rigid atoms, others: [36, 37, 38, 39, 40, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43]) total number of confs: 940 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300051 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300051 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300051/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300051/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300051 Building REAL300000300052 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300052' /scratch/stefan/7770550/working/building/REAL300000300052 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300052 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300052/0 /scratch/stefan/7770550/working/building/REAL300000300052 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/67 `/scratch/stefan/7770550/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300052 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 45, 1, 1, 33, 33, 33, 33, 33, 6, 1, 1, 9, 45, 45, 45, 45, 45, 1, 1] 145 rigid atoms, others: [33, 34, 41, 42, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300052 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 33, 33, 25, 33, 125, 125, 125, 145, 145, 33, 33, 2, 2, 2, 1, 1, 13, 33, 33, 125, 145, 145, 145, 145, 145, 33, 33] 145 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300052 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 145, 145, 145, 145, 145, 145, 145, 129, 80, 129, 129, 32, 9, 45, 45, 9, 9, 1, 9, 1, 1, 1, 45, 45, 145, 145, 145, 145, 145, 78, 45, 45, 9, 1, 1, 1, 1, 1, 45, 45] 145 rigid atoms, others: [36, 37, 38, 39, 40, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 561 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300052 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300052/1 /scratch/stefan/7770550/working/building/REAL300000300052 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/68 `/scratch/stefan/7770550/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300052.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300052 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 55, 55, 1, 1, 45, 45, 45, 45, 45, 1, 1, 9, 55, 55, 55, 55, 55, 1, 1] 165 rigid atoms, others: [32, 33, 40, 41, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300052 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 45, 45, 31, 45, 140, 140, 140, 165, 165, 45, 45, 2, 2, 2, 1, 1, 45, 45, 140, 165, 165, 165, 165, 165, 45, 45] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 504 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300052 none CC1=C(F)C=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 141, 91, 142, 142, 36, 14, 55, 55, 13, 13, 1, 13, 1, 1, 1, 55, 55, 165, 165, 165, 165, 165, 55, 55, 13, 1, 1, 1, 1, 1, 55, 55] 165 rigid atoms, others: [35, 36, 37, 38, 39, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 536 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300052 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300052 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300052/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300052/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300052 Building REAL300000300053 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300053' /scratch/stefan/7770550/working/building/REAL300000300053 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300053 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300053/0 /scratch/stefan/7770550/working/building/REAL300000300053 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/69 `/scratch/stefan/7770550/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])S1) `REAL300000300053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300053 none CC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 9, 50, 50, 50, 50, 50, 1, 1, 21] 113 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 17, 18, 38, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300053 none CC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 17, 21, 84, 84, 84, 113, 113, 21, 21, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 84, 113, 113, 113, 113, 113, 21, 21, 1] 113 rigid atoms, others: [0, 1, 2, 3, 39, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300053 none CC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 107, 83, 107, 106, 34, 13, 50, 50, 13, 13, 1, 13, 1, 1, 1, 50, 50, 113, 113, 113, 113, 113, 113, 113, 113, 113, 77, 50, 50, 13, 1, 1, 1, 1, 1, 50, 50, 113] 113 rigid atoms, others: [32, 33, 34, 35, 36, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 444 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300053 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300053/1 /scratch/stefan/7770550/working/building/REAL300000300053 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/70 `/scratch/stefan/7770550/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])S1) `REAL300000300053.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300053 none CC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 9, 9, 9, 51, 51, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 9, 51, 51, 51, 51, 51, 1, 1, 25] 131 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300053 none CC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 11, 25, 25, 16, 25, 83, 83, 83, 131, 131, 25, 25, 1, 1, 1, 1, 1, 1, 2, 2, 2, 25, 25, 83, 131, 131, 131, 131, 131, 25, 25, 1] 131 rigid atoms, others: [0, 1, 2, 3, 38, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300053 none CC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 123, 85, 123, 120, 35, 13, 51, 51, 13, 13, 1, 13, 1, 1, 1, 51, 51, 131, 131, 131, 131, 131, 131, 131, 131, 131, 51, 51, 13, 1, 1, 1, 1, 1, 51, 51, 131] 131 rigid atoms, others: [32, 33, 34, 35, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 440 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300053 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300053 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300053/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300053/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300053 Building REAL300000300054 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300054' /scratch/stefan/7770550/working/building/REAL300000300054 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300054 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300054/0 /scratch/stefan/7770550/working/building/REAL300000300054 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/71 `/scratch/stefan/7770550/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C(Cl)=C1) `REAL300000300054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300054 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 21, 23, 23, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 41, 1, 1, 23, 23, 23, 23, 23, 1, 1, 9, 41, 41, 41, 41, 41, 1, 1, 23] 101 rigid atoms, others: [36, 37, 10, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300054 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 11, 23, 23, 15, 22, 83, 83, 83, 101, 101, 23, 23, 1, 1, 1, 1, 1, 23, 23, 83, 101, 101, 101, 101, 101, 23, 23, 1] 101 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300054 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 101, 101, 101, 95, 71, 95, 94, 29, 16, 41, 41, 13, 13, 1, 13, 1, 1, 1, 41, 41, 101, 101, 101, 101, 101, 41, 41, 13, 1, 1, 1, 1, 1, 41, 41, 101] 101 rigid atoms, others: [32, 33, 34, 35, 16, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 313 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300054 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300054/1 /scratch/stefan/7770550/working/building/REAL300000300054 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/72 `/scratch/stefan/7770550/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(Cl)=C1) `REAL300000300054.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300054 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 17, 19, 19, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 41, 1, 1, 19, 19, 19, 19, 19, 6, 1, 1, 9, 41, 41, 41, 41, 41, 1, 1, 19] 100 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300054 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 15, 19, 78, 78, 78, 100, 100, 19, 19, 1, 1, 1, 1, 1, 9, 19, 19, 78, 100, 100, 100, 100, 100, 19, 19, 1] 100 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300054 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 94, 70, 94, 93, 30, 13, 41, 41, 13, 13, 1, 13, 1, 1, 1, 41, 41, 100, 100, 100, 100, 100, 67, 41, 41, 13, 1, 1, 1, 1, 1, 41, 41, 100] 100 rigid atoms, others: [32, 33, 34, 35, 36, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 372 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300054 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300054 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300054/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300054/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300054 Building REAL300000300055 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300055' /scratch/stefan/7770550/working/building/REAL300000300055 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300055 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300055/0 /scratch/stefan/7770550/working/building/REAL300000300055 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/73 `/scratch/stefan/7770550/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1F) `REAL300000300055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300055 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 17, 33, 17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 1, 1, 17, 17, 17, 17, 17, 4, 1, 1, 9, 37, 37, 37, 37, 37, 1, 1, 17] 201 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300055 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 13, 17, 95, 95, 95, 201, 201, 17, 17, 1, 1, 1, 1, 1, 9, 17, 17, 95, 201, 201, 201, 201, 201, 17, 17, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300055 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 103, 55, 103, 103, 31, 13, 37, 37, 13, 13, 1, 13, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 54, 37, 37, 13, 1, 1, 1, 1, 1, 37, 37, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 633 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300055 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300055/1 /scratch/stefan/7770550/working/building/REAL300000300055 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/74 `/scratch/stefan/7770550/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1F) `REAL300000300055.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300055 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 20, 36, 20, 20, 20, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 9, 9, 9, 38, 38, 1, 1, 20, 20, 20, 20, 20, 1, 1, 9, 38, 38, 38, 38, 38, 1, 1, 20] 201 rigid atoms, others: [36, 37, 10, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300055 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 20, 20, 14, 20, 99, 99, 99, 201, 201, 20, 20, 1, 1, 1, 1, 1, 20, 20, 99, 201, 201, 201, 201, 201, 20, 20, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300055 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 110, 57, 110, 110, 28, 10, 38, 38, 10, 10, 1, 10, 1, 1, 1, 38, 38, 201, 201, 201, 201, 201, 38, 38, 10, 1, 1, 1, 1, 1, 38, 38, 201] 201 rigid atoms, others: [32, 33, 34, 35, 16, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 605 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300055 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300055 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300055/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300055/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300055 Building REAL300000300056 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300056' /scratch/stefan/7770550/working/building/REAL300000300056 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300056 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300056/0 /scratch/stefan/7770550/working/building/REAL300000300056 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/75 `/scratch/stefan/7770550/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)S1) `REAL300000300056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300056 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 52, 1, 1, 57, 57, 57, 1, 1, 10, 52, 52, 52, 52, 52, 1, 1] 201 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 21, 22, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300056 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 6, 25, 57, 57, 38, 57, 139, 139, 139, 201, 201, 57, 57, 1, 1, 1, 57, 57, 139, 201, 201, 201, 201, 201, 57, 57] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 686 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300056 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 165, 105, 164, 164, 37, 11, 52, 52, 11, 11, 1, 11, 1, 1, 1, 52, 52, 201, 201, 201, 52, 52, 11, 1, 1, 1, 1, 1, 52, 52] 201 rigid atoms, others: [32, 33, 16, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 638 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300056 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300056 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300056/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300056 Building REAL300000300057 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300057' /scratch/stefan/7770550/working/building/REAL300000300057 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300057 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300057/0 /scratch/stefan/7770550/working/building/REAL300000300057 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/76 `/scratch/stefan/7770550/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300057 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 45, 1, 1, 29, 29, 29, 6, 1, 1, 9, 45, 45, 45, 45, 45, 1, 1, 29] 131 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300057 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 21, 29, 105, 105, 105, 131, 131, 29, 29, 1, 1, 1, 9, 29, 29, 105, 131, 131, 131, 131, 131, 29, 29, 1] 131 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 25, 26, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300057 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 131, 131, 131, 108, 63, 108, 108, 45, 31, 45, 45, 11, 11, 1, 11, 1, 1, 1, 45, 45, 131, 131, 131, 63, 45, 45, 11, 1, 1, 1, 1, 1, 45, 45, 131] 131 rigid atoms, others: [32, 33, 34, 35, 36, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 482 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300057 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300057/1 /scratch/stefan/7770550/working/building/REAL300000300057 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/77 `/scratch/stefan/7770550/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300057.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300057 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 10, 10, 10, 40, 40, 1, 1, 29, 29, 29, 1, 1, 10, 40, 40, 40, 40, 40, 1, 1, 29] 124 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300057 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 29, 29, 17, 29, 102, 102, 102, 124, 124, 29, 29, 1, 1, 1, 29, 29, 102, 124, 124, 124, 124, 124, 29, 29, 1] 124 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 38, 25, 26, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300057 none O=C([O-])C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 124, 124, 124, 124, 101, 62, 101, 101, 40, 29, 40, 40, 9, 9, 1, 9, 1, 1, 1, 40, 40, 124, 124, 124, 40, 40, 9, 1, 1, 1, 1, 1, 40, 40, 124] 124 rigid atoms, others: [32, 33, 34, 35, 18, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 408 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300057 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300057 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300057/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300057/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300057 Building REAL300000300058 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300058' /scratch/stefan/7770550/working/building/REAL300000300058 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300058 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300058/0 /scratch/stefan/7770550/working/building/REAL300000300058 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/78 `/scratch/stefan/7770550/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1F) `REAL300000300058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300058 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 61, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 54, 54, 1, 1, 61, 61, 61, 61, 61, 61, 61, 1, 1, 9, 54, 54, 54, 54, 54, 1, 1] 201 rigid atoms, others: [32, 33, 40, 41, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300058 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 61, 61, 41, 61, 177, 177, 177, 201, 201, 61, 61, 1, 1, 2, 2, 2, 1, 1, 61, 61, 177, 201, 201, 201, 201, 201, 61, 61] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300058 none CC1=CC(C(=O)[O-])=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 150, 94, 151, 151, 37, 11, 54, 54, 11, 11, 1, 11, 1, 1, 1, 54, 54, 201, 201, 201, 201, 201, 201, 201, 54, 54, 11, 1, 1, 1, 1, 1, 54, 54] 201 rigid atoms, others: [35, 36, 37, 38, 39, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 637 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300058 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300058 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300058/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300058 Building REAL300000300059 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300059' /scratch/stefan/7770550/working/building/REAL300000300059 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300059 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300059/0 /scratch/stefan/7770550/working/building/REAL300000300059 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/79 `/scratch/stefan/7770550/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C(F)=C1) `REAL300000300059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300059 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 27, 57, 57, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 57, 57, 1, 1, 57, 57, 57, 57, 57, 1, 1, 9, 57, 57, 57, 57, 57, 1, 1, 57] 201 rigid atoms, others: [36, 37, 10, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300059 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 25, 57, 57, 40, 57, 169, 169, 169, 201, 201, 57, 57, 1, 1, 1, 1, 1, 57, 57, 169, 201, 201, 201, 201, 201, 57, 57, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300059 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 152, 95, 151, 152, 38, 13, 57, 57, 13, 13, 1, 13, 1, 1, 1, 57, 57, 201, 201, 201, 201, 201, 57, 57, 13, 1, 1, 1, 1, 1, 57, 57, 201] 201 rigid atoms, others: [32, 33, 34, 35, 16, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 655 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300059 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300059/1 /scratch/stefan/7770550/working/building/REAL300000300059 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/80 `/scratch/stefan/7770550/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(F)=C1) `REAL300000300059.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300059 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 27, 57, 57, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 55, 55, 1, 1, 57, 57, 57, 57, 57, 6, 1, 1, 9, 55, 55, 55, 55, 55, 1, 1, 57] 201 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300059 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 25, 57, 57, 42, 57, 173, 173, 173, 201, 201, 57, 57, 1, 1, 1, 1, 1, 25, 57, 57, 173, 201, 201, 201, 201, 201, 57, 57, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300059 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 169, 107, 167, 167, 37, 11, 55, 55, 11, 11, 1, 11, 1, 1, 1, 55, 55, 201, 201, 201, 201, 201, 103, 55, 55, 11, 1, 1, 1, 1, 1, 55, 55, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 744 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300059 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300059 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300059/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300059/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300059 Building REAL300000300060 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300060' /scratch/stefan/7770550/working/building/REAL300000300060 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300060 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300060/0 /scratch/stefan/7770550/working/building/REAL300000300060 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/81 `/scratch/stefan/7770550/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1Cl) `REAL300000300060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300060 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [34, 22, 34, 22, 22, 22, 12, 5, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 9, 40, 40, 1, 1, 22, 22, 22, 22, 22, 5, 1, 1, 9, 40, 40, 40, 40, 40, 1, 1, 22] 162 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300060 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 22, 22, 16, 22, 88, 88, 88, 162, 162, 22, 22, 1, 1, 1, 1, 1, 9, 22, 22, 88, 162, 162, 162, 162, 162, 22, 22, 1] 162 rigid atoms, others: [1, 3, 4, 5, 6, 7, 39, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300060 none O=C([O-])C1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 162, 162, 84, 60, 84, 84, 28, 15, 40, 40, 11, 11, 1, 11, 1, 1, 1, 40, 40, 162, 162, 162, 162, 162, 58, 40, 40, 11, 1, 1, 1, 1, 1, 40, 40, 162] 162 rigid atoms, others: [32, 33, 34, 35, 36, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 505 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300060 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300060/1 /scratch/stefan/7770550/working/building/REAL300000300060 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/82 `/scratch/stefan/7770550/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1Cl) `REAL300000300060.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300060 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 29, 43, 29, 29, 29, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 43, 1, 1, 29, 29, 29, 29, 29, 1, 1, 9, 43, 43, 43, 43, 43, 1, 1, 29] 188 rigid atoms, others: [36, 37, 10, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300060 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 17, 29, 106, 106, 106, 188, 188, 29, 29, 1, 1, 1, 1, 1, 29, 29, 106, 188, 188, 188, 188, 188, 29, 29, 1] 188 rigid atoms, others: [1, 3, 4, 5, 6, 7, 38, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300060 none O=C([O-])C1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1Cl NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 188, 188, 104, 62, 104, 104, 29, 13, 43, 43, 13, 13, 1, 13, 1, 1, 1, 43, 43, 188, 188, 188, 188, 188, 43, 43, 13, 1, 1, 1, 1, 1, 43, 43, 188] 188 rigid atoms, others: [32, 33, 34, 35, 16, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 569 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300060 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300060 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300060/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300060/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300060 Building REAL300000300061 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300061' /scratch/stefan/7770550/working/building/REAL300000300061 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300061 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300061/0 /scratch/stefan/7770550/working/building/REAL300000300061 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/83 `/scratch/stefan/7770550/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(F)=C1F) `REAL300000300061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300061 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 25, 47, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 1, 1, 25, 25, 25, 25, 25, 25, 6, 1, 1, 9, 37, 37, 37, 37, 37, 1, 1, 25] 201 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300061 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 18, 25, 103, 103, 103, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 9, 25, 25, 103, 201, 201, 201, 201, 201, 25, 25, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 22, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300061 none O=C([O-])C1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 128, 67, 128, 128, 30, 13, 37, 37, 11, 11, 1, 11, 1, 1, 1, 37, 37, 201, 201, 201, 201, 201, 201, 66, 37, 37, 11, 1, 1, 1, 1, 1, 37, 37, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 671 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300061 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300061/1 /scratch/stefan/7770550/working/building/REAL300000300061 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/84 `/scratch/stefan/7770550/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CC(F)=C1F) `REAL300000300061.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300061 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 25, 45, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 39, 39, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 9, 39, 39, 39, 39, 39, 1, 1, 25] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300061 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 16, 25, 104, 104, 104, 201, 201, 25, 25, 1, 1, 1, 1, 1, 1, 25, 25, 104, 201, 201, 201, 201, 201, 25, 25, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 38, 22, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300061 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 130, 72, 130, 130, 31, 13, 39, 39, 13, 13, 1, 13, 1, 1, 1, 39, 39, 201, 201, 201, 201, 201, 201, 39, 39, 13, 1, 1, 1, 1, 1, 39, 39, 201] 201 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 613 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300061 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300061 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300061/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300061/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300061 Building REAL300000300062 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300062' /scratch/stefan/7770550/working/building/REAL300000300062 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300062 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300062/0 /scratch/stefan/7770550/working/building/REAL300000300062 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/85 `/scratch/stefan/7770550/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300062 none O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 53, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 53, 53, 1, 1, 53, 53, 53, 106, 1, 1, 9, 53, 53, 53, 53, 53, 1, 1, 53] 402 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300062 none O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 53, 53, 38, 53, 160, 160, 160, 201, 201, 53, 53, 1, 1, 1, 2, 53, 53, 160, 201, 201, 201, 201, 201, 53, 53, 1] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 25, 26, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300000300062 none O=C([O-])C1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 164, 98, 164, 164, 38, 13, 53, 53, 13, 13, 1, 13, 1, 1, 1, 53, 53, 201, 201, 201, 402, 53, 53, 13, 1, 1, 1, 1, 1, 53, 53, 201] 402 rigid atoms, others: [32, 33, 34, 35, 36, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 1074 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300062 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300062/1 /scratch/stefan/7770550/working/building/REAL300000300062 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/86 `/scratch/stefan/7770550/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300062.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300062 none O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 38, 38, 1, 1, 18, 18, 18, 6, 1, 1, 9, 38, 38, 38, 38, 38, 1, 1, 18] 76 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 17, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300062 none O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 18, 18, 6, 6, 42, 46, 54, 76, 76, 18, 18, 1, 1, 1, 6, 18, 18, 42, 76, 76, 76, 76, 76, 18, 18, 1] 76 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300062 none O=C([O-])C1=CC=C([O-])C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 76, 76, 76, 76, 76, 76, 55, 76, 76, 30, 30, 38, 38, 13, 13, 1, 13, 1, 1, 1, 38, 38, 76, 76, 76, 55, 38, 38, 13, 1, 1, 1, 1, 1, 38, 38, 76] 76 rigid atoms, others: [32, 33, 34, 35, 36, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 281 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300062 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300062 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300062/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300062/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300062 Building REAL300000300063 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300063' /scratch/stefan/7770550/working/building/REAL300000300063 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300063 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300063/0 /scratch/stefan/7770550/working/building/REAL300000300063 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/87 `/scratch/stefan/7770550/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1) `REAL300000300063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300063 none O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [38, 19, 38, 11, 11, 19, 19, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 34, 1, 1, 19, 19, 19, 19, 19, 19, 4, 1, 1, 9, 34, 34, 34, 34, 34, 1, 1, 19, 19] 123 rigid atoms, others: [32, 39, 40, 11, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300063 none O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 9, 9, 70, 70, 73, 123, 123, 19, 19, 1, 1, 2, 2, 1, 1, 9, 19, 19, 70, 123, 123, 123, 123, 123, 19, 19, 1, 1] 123 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 42, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300063 none O=C([O-])CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 74, 74, 123, 123, 74, 47, 74, 74, 27, 27, 34, 34, 12, 12, 1, 12, 1, 1, 1, 34, 34, 123, 123, 123, 123, 123, 123, 47, 34, 34, 12, 1, 1, 1, 1, 1, 34, 34, 123, 123] 123 rigid atoms, others: [34, 35, 36, 37, 38, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42]) total number of confs: 805 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300063 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300063/1 /scratch/stefan/7770550/working/building/REAL300000300063 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/88 `/scratch/stefan/7770550/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1) `REAL300000300063.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300063 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [34, 17, 34, 9, 9, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 37, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 9, 37, 37, 37, 37, 37, 1, 1, 17, 17] 121 rigid atoms, others: [38, 39, 11, 12, 13, 14, 15, 16, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300063 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 13, 13, 82, 82, 82, 121, 121, 17, 17, 1, 1, 2, 2, 1, 1, 17, 17, 82, 121, 121, 121, 121, 121, 17, 17, 1, 1] 121 rigid atoms, others: [3, 4, 5, 6, 7, 8, 41, 40, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300063 none O=C([O-])CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 86, 86, 121, 121, 86, 55, 86, 86, 29, 21, 37, 37, 9, 9, 1, 9, 1, 1, 1, 37, 37, 121, 121, 121, 121, 121, 121, 37, 37, 9, 1, 1, 1, 1, 1, 37, 37, 121, 121] 121 rigid atoms, others: [33, 34, 35, 36, 37, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 694 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300063 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300063 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300063/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300063/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300063 Building REAL300000300064 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300064' /scratch/stefan/7770550/working/building/REAL300000300064 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300064 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300064/0 /scratch/stefan/7770550/working/building/REAL300000300064 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/89 `/scratch/stefan/7770550/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300064 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 5, 14, 14, 1, 1, 1, 1, 1, 1, 9, 9, 9, 40, 40, 1, 1, 23, 23, 23, 23, 23, 23, 5, 1, 1, 9, 40, 40, 40, 40, 40, 1, 1] 100 rigid atoms, others: [33, 34, 41, 42, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300064 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 11, 23, 23, 18, 18, 80, 80, 80, 100, 100, 23, 23, 2, 2, 2, 1, 1, 1, 11, 23, 23, 80, 100, 100, 100, 100, 100, 23, 23] 100 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 29, 30, 31] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300064 none CC1=C(C(=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 100, 100, 98, 61, 98, 98, 40, 28, 40, 40, 11, 11, 1, 11, 1, 1, 1, 40, 40, 100, 100, 100, 100, 100, 100, 61, 40, 40, 11, 1, 1, 1, 1, 1, 40, 40] 100 rigid atoms, others: [36, 37, 38, 39, 40, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 387 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300064 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300064 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300064/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300064 Building REAL300000300065 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300065' /scratch/stefan/7770550/working/building/REAL300000300065 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300065 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300065/0 /scratch/stefan/7770550/working/building/REAL300000300065 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/90 `/scratch/stefan/7770550/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(C(=O)[O-])=C1F) `REAL300000300065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300065 none CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 41, 1, 1, 25, 25, 25, 47, 47, 25, 25, 25, 25, 25, 25, 6, 1, 1, 9, 41, 41, 41, 41, 41, 1, 1, 25] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 40, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300065 none CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 25, 25, 18, 25, 107, 107, 107, 201, 201, 25, 25, 1, 1, 1, 3, 3, 1, 1, 2, 2, 2, 1, 9, 25, 25, 107, 201, 201, 201, 201, 201, 25, 25, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 42, 20, 21, 22, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300065 none CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 138, 72, 139, 138, 35, 14, 41, 41, 13, 13, 1, 13, 1, 1, 1, 41, 41, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 41, 41, 13, 1, 1, 1, 1, 1, 41, 41, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 687 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300065 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300065 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300065/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300065 Building REAL300000300066 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300066' /scratch/stefan/7770550/working/building/REAL300000300066 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300066 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300066/0 /scratch/stefan/7770550/working/building/REAL300000300066 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/91 `/scratch/stefan/7770550/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300066 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 15, 18, 24, 24, 24, 24, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 49, 1, 1, 24, 24, 24, 24, 24, 24, 6, 1, 1, 9, 49, 49, 49, 49, 49, 1, 1] 110 rigid atoms, others: [33, 34, 41, 42, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300066 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 24, 24, 12, 12, 66, 66, 66, 110, 110, 24, 24, 2, 2, 2, 1, 1, 1, 12, 24, 24, 66, 110, 110, 110, 110, 110, 24, 24] 110 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300066 none CC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 104, 110, 110, 110, 110, 110, 103, 71, 103, 103, 18, 15, 49, 49, 13, 13, 1, 13, 1, 1, 1, 49, 49, 110, 110, 110, 110, 110, 110, 70, 49, 49, 13, 1, 1, 1, 1, 1, 49, 49] 110 rigid atoms, others: [36, 37, 38, 39, 40, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 463 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300066 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300066 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300066/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300066 Building REAL300000300067 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300067' /scratch/stefan/7770550/working/building/REAL300000300067 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300067 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300067/0 /scratch/stefan/7770550/working/building/REAL300000300067 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/92 `/scratch/stefan/7770550/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(C(=O)[O-])=C1C) `REAL300000300067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300067 none CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 1, 1, 9, 28, 28, 28, 28, 28, 1, 1, 27, 27, 27, 27] 107 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 40, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300067 none CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 19, 27, 93, 93, 93, 107, 107, 27, 27, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 1, 9, 27, 27, 93, 107, 107, 107, 107, 107, 27, 27, 1, 2, 2, 2] 107 rigid atoms, others: [0, 1, 2, 3, 4, 42, 20, 21, 22, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300067 none CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 69, 47, 69, 69, 22, 7, 28, 28, 7, 7, 1, 7, 1, 1, 1, 28, 28, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 46, 28, 28, 7, 1, 1, 1, 1, 1, 28, 28, 107, 107, 107, 107] 107 rigid atoms, others: [35, 36, 37, 38, 39, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45]) total number of confs: 361 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300067 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300067 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300067/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300067 Building REAL300000300068 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300068' /scratch/stefan/7770550/working/building/REAL300000300068 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300068 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300068/0 /scratch/stefan/7770550/working/building/REAL300000300068 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/93 `/scratch/stefan/7770550/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(F)=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300068 none O=C([O-])C1=CC(F)=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 58, 58, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 55, 55, 1, 1, 58, 58, 1, 1, 9, 55, 55, 55, 55, 55, 1, 1, 58] 201 rigid atoms, others: [36, 37, 13, 14, 15, 16, 17, 18, 24, 25, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300068 none O=C([O-])C1=CC(F)=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 58, 58, 39, 58, 175, 175, 175, 201, 201, 58, 58, 1, 1, 58, 58, 175, 201, 201, 201, 201, 201, 58, 58, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 38, 26, 27] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300068 none O=C([O-])C1=CC(F)=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 15, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 91, 143, 145, 34, 11, 55, 55, 11, 11, 1, 11, 1, 1, 1, 55, 55, 201, 201, 55, 55, 11, 1, 1, 1, 1, 1, 55, 55, 201] 201 rigid atoms, others: [32, 33, 34, 35, 19, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 635 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300068 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300068 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300068/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300068 Building REAL300000300069 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300069' /scratch/stefan/7770550/working/building/REAL300000300069 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300069 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300069/0 /scratch/stefan/7770550/working/building/REAL300000300069 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/94 `/scratch/stefan/7770550/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(C)=C1C(=O)[O-]) `REAL300000300069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300069 none CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 25, 25, 25, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 36, 36, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 1, 1, 9, 36, 36, 36, 36, 36, 1, 1, 25, 25, 25] 97 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 19, 20, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300069 none CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 5, 5, 5, 11, 25, 25, 20, 25, 87, 87, 87, 97, 97, 25, 25, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 11, 25, 25, 87, 97, 97, 97, 97, 97, 25, 25, 2, 2, 2] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 21, 22, 23, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300069 none CC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 97, 95, 60, 95, 95, 27, 11, 36, 36, 11, 11, 1, 11, 1, 1, 1, 36, 36, 97, 97, 97, 97, 97, 97, 97, 97, 97, 96, 97, 60, 36, 36, 11, 1, 1, 1, 1, 1, 36, 36, 97, 97, 97] 97 rigid atoms, others: [36, 37, 38, 39, 40, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45]) total number of confs: 378 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300069 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300069 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300069/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300069 Building REAL300000300070 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300070' /scratch/stefan/7770550/working/building/REAL300000300070 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300070 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300070/0 /scratch/stefan/7770550/working/building/REAL300000300070 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/95 `/scratch/stefan/7770550/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300070 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 49, 1, 1, 51, 51, 51, 79, 79, 51, 51, 51, 51, 1, 1, 9, 49, 49, 49, 49, 49, 1, 1, 51] 201 rigid atoms, others: [32, 39, 40, 9, 10, 11, 12, 13, 14, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300070 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 51, 51, 32, 25, 118, 119, 120, 201, 201, 51, 51, 1, 1, 1, 3, 3, 2, 2, 2, 1, 51, 51, 118, 201, 201, 201, 201, 201, 51, 51, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 22, 23, 24, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 680 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300070 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 124, 77, 125, 124, 37, 37, 49, 49, 13, 13, 1, 13, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 49, 49, 13, 1, 1, 1, 1, 1, 49, 49, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 536 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300070 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300070/1 /scratch/stefan/7770550/working/building/REAL300000300070 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/96 `/scratch/stefan/7770550/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300070.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300070 none CC1=CC(F)=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 9, 9, 9, 52, 52, 1, 1, 45, 45, 45, 77, 77, 45, 45, 45, 45, 4, 1, 1, 9, 52, 52, 52, 52, 52, 1, 1, 45] 201 rigid atoms, others: [32, 33, 40, 9, 10, 11, 12, 13, 14, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300070 none CC1=CC(F)=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 45, 45, 35, 25, 115, 118, 115, 201, 201, 45, 45, 1, 1, 1, 3, 3, 2, 2, 2, 1, 25, 45, 45, 115, 201, 201, 201, 201, 201, 45, 45, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 22, 23, 24, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300070 none CC1=CC(F)=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 126, 87, 126, 126, 47, 38, 52, 52, 12, 12, 1, 12, 1, 1, 1, 52, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 52, 52, 12, 1, 1, 1, 1, 1, 52, 52, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 575 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300070 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300070 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300070/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300070/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300070 Building REAL300000300071 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300071' /scratch/stefan/7770550/working/building/REAL300000300071 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300071 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300071/0 /scratch/stefan/7770550/working/building/REAL300000300071 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/97 `/scratch/stefan/7770550/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300071 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 75, 75, 39, 39, 12, 4, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 9, 39, 39, 1, 1, 39, 39, 39, 39, 39, 1, 1, 9, 39, 39, 39, 39, 39, 1, 1, 39] 201 rigid atoms, others: [32, 39, 40, 13, 14, 15, 16, 17, 18, 24, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300071 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 22, 39, 39, 22, 22, 95, 95, 96, 201, 201, 39, 39, 1, 2, 2, 2, 1, 39, 39, 95, 201, 201, 201, 201, 201, 39, 39, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 41, 26, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 661 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300071 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 54, 111, 111, 11, 11, 39, 39, 11, 11, 1, 11, 1, 1, 1, 39, 39, 201, 201, 201, 201, 201, 39, 39, 11, 1, 1, 1, 1, 1, 39, 39, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 564 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300071 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300071 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300071/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300071 Building REAL300000300072 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300072' /scratch/stefan/7770550/working/building/REAL300000300072 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300072 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300072/0 /scratch/stefan/7770550/working/building/REAL300000300072 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/98 `/scratch/stefan/7770550/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300072 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 21, 21, 21, 21, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 34, 1, 1, 21, 21, 21, 27, 27, 53, 53, 53, 53, 53, 21, 21, 4, 1, 1, 9, 34, 34, 34, 34, 34, 1, 1, 21] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 44, 43, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300072 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 9, 21, 21, 15, 15, 74, 72, 74, 103, 103, 21, 21, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 1, 1, 9, 21, 21, 70, 103, 103, 103, 103, 103, 21, 21, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 45, 22, 23, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300072 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 103, 103, 103, 103, 76, 50, 77, 77, 26, 15, 34, 34, 10, 10, 1, 10, 1, 1, 1, 34, 34, 103, 103, 103, 115, 115, 201, 201, 201, 201, 201, 103, 103, 50, 34, 34, 10, 1, 1, 1, 1, 1, 34, 34, 103] 201 rigid atoms, others: [38, 39, 40, 41, 42, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45]) total number of confs: 977 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300072 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300072 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300072/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300072 Building REAL300000300073 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300073' /scratch/stefan/7770550/working/building/REAL300000300073 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300073 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300073/0 /scratch/stefan/7770550/working/building/REAL300000300073 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/99 `/scratch/stefan/7770550/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300073 none CCN1C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 21, 21, 21, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 9, 9, 9, 42, 42, 1, 1, 21, 21, 21, 21, 21, 57, 57, 57, 57, 57, 21, 4, 1, 1, 9, 42, 42, 42, 42, 42, 1, 1, 21] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 19, 20, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300073 none CCN1C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 15, 21, 71, 71, 71, 121, 121, 21, 21, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 9, 21, 21, 71, 121, 121, 121, 121, 121, 21, 21, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 43, 21, 22, 23, 24, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300073 none CCN1C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 121, 121, 121, 93, 58, 93, 93, 32, 13, 42, 42, 13, 13, 1, 13, 1, 1, 1, 42, 42, 121, 121, 121, 121, 121, 201, 201, 201, 201, 201, 121, 58, 42, 42, 13, 1, 1, 1, 1, 1, 42, 42, 121] 201 rigid atoms, others: [36, 37, 38, 39, 40, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43]) total number of confs: 921 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300073 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300073/1 /scratch/stefan/7770550/working/building/REAL300000300073 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/100 `/scratch/stefan/7770550/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300073.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300073 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 21, 21, 21, 11, 4, 11, 11, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 34, 1, 1, 21, 21, 21, 21, 21, 56, 56, 56, 56, 56, 21, 1, 1, 9, 34, 34, 34, 34, 34, 1, 1, 21] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 40, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 302 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300073 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 15, 21, 73, 73, 73, 124, 124, 21, 21, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 21, 21, 73, 124, 124, 124, 124, 124, 21, 21, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 42, 21, 22, 23, 24, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300073 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 124, 124, 124, 84, 56, 84, 84, 26, 9, 34, 34, 9, 9, 1, 9, 1, 1, 1, 34, 34, 124, 124, 124, 124, 124, 201, 201, 201, 201, 201, 124, 34, 34, 9, 1, 1, 1, 1, 1, 34, 34, 124] 201 rigid atoms, others: [35, 36, 37, 38, 39, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 848 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300073 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300073 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300073/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300073/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300073 Building REAL300000300074 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300074' /scratch/stefan/7770550/working/building/REAL300000300074 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300074 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300074/0 /scratch/stefan/7770550/working/building/REAL300000300074 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/101 `/scratch/stefan/7770550/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1C(=O)[O-]) `REAL300000300074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300074 none CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 11, 11, 11, 44, 44, 1, 1, 17, 17, 17, 17, 33, 33, 17, 17, 17, 17, 4, 1, 1, 11, 44, 44, 44, 44, 44, 1, 1, 17, 17] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 40, 18, 19, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300074 none CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 17, 17, 13, 13, 99, 94, 99, 201, 201, 17, 17, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 17, 17, 96, 201, 201, 201, 201, 201, 17, 17, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 20, 21, 22, 23, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300074 none CC1=CC(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 60, 111, 111, 42, 37, 44, 44, 13, 13, 1, 13, 1, 1, 1, 44, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 44, 44, 13, 1, 1, 1, 1, 1, 44, 44, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42]) total number of confs: 588 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300074 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300074 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300074/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300074 Building REAL300000300075 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300075' /scratch/stefan/7770550/working/building/REAL300000300075 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300075 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300075/0 /scratch/stefan/7770550/working/building/REAL300000300075 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/102 `/scratch/stefan/7770550/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300075 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 57, 57, 31, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 45, 1, 1, 31, 31, 31, 31, 31, 6, 1, 1, 9, 45, 45, 45, 45, 45, 1, 1] 201 rigid atoms, others: [33, 34, 41, 42, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300075 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 5, 5, 5, 13, 31, 31, 20, 13, 80, 92, 100, 201, 201, 31, 31, 2, 2, 2, 1, 1, 13, 31, 31, 80, 201, 201, 201, 201, 201, 31, 31] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 9, 10, 11, 30, 31] set([7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300075 none CC1=CC(F)=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 81, 140, 140, 44, 35, 45, 45, 11, 11, 1, 11, 1, 1, 1, 45, 45, 201, 201, 201, 201, 201, 81, 45, 45, 11, 1, 1, 1, 1, 1, 45, 45] 201 rigid atoms, others: [36, 37, 38, 39, 40, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 620 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300075 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300075 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300075/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300075 Building REAL300000300076 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300076' /scratch/stefan/7770550/working/building/REAL300000300076 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300076 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300076/0 /scratch/stefan/7770550/working/building/REAL300000300076 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/103 `/scratch/stefan/7770550/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1F) `REAL300000300076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300076 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 38, 68, 38, 38, 38, 38, 12, 4, 12, 12, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 49, 1, 1, 38, 38, 38, 38, 38, 1, 1, 9, 49, 49, 49, 49, 49, 1, 1] 201 rigid atoms, others: [37, 38, 11, 12, 13, 14, 15, 16, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300076 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 38, 38, 29, 38, 102, 102, 102, 201, 201, 38, 38, 1, 1, 1, 1, 1, 38, 38, 102, 201, 201, 201, 201, 201, 38, 38] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 642 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300076 none O=C([O-])C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 148, 84, 148, 148, 37, 15, 49, 49, 11, 11, 1, 11, 1, 1, 1, 49, 49, 201, 201, 201, 201, 201, 49, 49, 11, 1, 1, 1, 1, 1, 49, 49] 201 rigid atoms, others: [32, 33, 34, 35, 36, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 617 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300076 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300076 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300076/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300076 Building REAL300000300077 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300077' /scratch/stefan/7770550/working/building/REAL300000300077 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300077 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300077/0 /scratch/stefan/7770550/working/building/REAL300000300077 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/104 `/scratch/stefan/7770550/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300077 none CC1=C(F)C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 25, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 48, 48, 1, 1, 25, 25, 25, 49, 49, 25, 25, 25, 25, 6, 1, 1, 9, 48, 48, 48, 48, 48, 1, 1, 25] 201 rigid atoms, others: [32, 33, 40, 9, 10, 11, 12, 13, 14, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300077 none CC1=C(F)C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 25, 25, 18, 25, 105, 105, 105, 201, 201, 25, 25, 1, 1, 1, 3, 3, 2, 2, 2, 1, 9, 25, 25, 105, 201, 201, 201, 201, 201, 25, 25, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 22, 23, 24, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300077 none CC1=C(F)C=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 141, 77, 141, 140, 38, 13, 48, 48, 13, 13, 1, 13, 1, 1, 1, 48, 48, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 48, 48, 13, 1, 1, 1, 1, 1, 48, 48, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 721 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300077 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300077/1 /scratch/stefan/7770550/working/building/REAL300000300077 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/105 `/scratch/stefan/7770550/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-]) `REAL300000300077.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300077 none CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 46, 46, 1, 1, 27, 27, 27, 47, 47, 27, 27, 27, 27, 1, 1, 9, 46, 46, 46, 46, 46, 1, 1, 27] 201 rigid atoms, others: [32, 39, 40, 9, 10, 11, 12, 13, 14, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300077 none CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 16, 27, 111, 111, 111, 201, 201, 27, 27, 1, 1, 1, 3, 3, 2, 2, 2, 1, 27, 27, 111, 201, 201, 201, 201, 201, 27, 27, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 22, 23, 24, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 611 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300077 none CC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 151, 77, 151, 151, 34, 13, 46, 46, 13, 13, 1, 13, 1, 1, 1, 46, 46, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 46, 13, 1, 1, 1, 1, 1, 46, 46, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 687 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300077 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300077 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300077/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300077/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300077 Building REAL300000300078 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300078' /scratch/stefan/7770550/working/building/REAL300000300078 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300078 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300078/0 /scratch/stefan/7770550/working/building/REAL300000300078 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/106 `/scratch/stefan/7770550/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1) `REAL300000300078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300078 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 1, 1, 59, 59, 59, 1, 1, 9, 50, 50, 50, 50, 50, 1, 1, 59] 201 rigid atoms, others: [35, 36, 11, 12, 13, 14, 15, 16, 22, 23, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300078 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 59, 59, 41, 59, 141, 141, 141, 201, 201, 59, 59, 1, 1, 1, 59, 59, 141, 201, 201, 201, 201, 201, 59, 59, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 37] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300078 none O=C([O-])C1=CC=NC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 141, 87, 139, 139, 37, 13, 50, 50, 11, 11, 1, 11, 1, 1, 1, 50, 50, 201, 201, 201, 50, 50, 11, 1, 1, 1, 1, 1, 50, 50, 201] 201 rigid atoms, others: [32, 33, 34, 17, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 605 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300078 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300078 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300078/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300078 Building REAL300000300079 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300079' /scratch/stefan/7770550/working/building/REAL300000300079 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300079 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300079/0 /scratch/stefan/7770550/working/building/REAL300000300079 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/107 `/scratch/stefan/7770550/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300079 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 48, 48, 48, 23, 48, 48, 48, 48, 48, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 9, 9, 9, 53, 53, 1, 1, 81, 81, 81, 48, 48, 48, 1, 1, 9, 53, 53, 53, 53, 53, 1, 1] 201 rigid atoms, others: [33, 34, 41, 42, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300079 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 23, 48, 48, 36, 48, 147, 147, 147, 201, 201, 48, 48, 3, 3, 3, 1, 1, 1, 48, 48, 147, 201, 201, 201, 201, 201, 48, 48] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 8, 9, 10, 11, 30, 31] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300079 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 186, 201, 201, 201, 201, 201, 146, 85, 145, 145, 35, 11, 53, 53, 11, 11, 1, 11, 1, 1, 1, 53, 53, 201, 201, 201, 201, 201, 201, 53, 53, 11, 1, 1, 1, 1, 1, 53, 53] 201 rigid atoms, others: [36, 37, 38, 39, 40, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42]) total number of confs: 695 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300079 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300079/1 /scratch/stefan/7770550/working/building/REAL300000300079 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/108 `/scratch/stefan/7770550/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1) `REAL300000300079.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300079 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 52, 52, 52, 27, 52, 52, 52, 52, 52, 17, 6, 17, 17, 1, 1, 1, 1, 1, 1, 9, 9, 9, 56, 56, 1, 1, 58, 58, 58, 52, 52, 52, 6, 1, 1, 9, 56, 56, 56, 56, 56, 1, 1] 201 rigid atoms, others: [34, 35, 42, 43, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300079 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 24, 52, 52, 40, 51, 169, 169, 169, 201, 201, 52, 52, 4, 4, 4, 1, 1, 1, 24, 52, 52, 169, 201, 201, 201, 201, 201, 52, 52] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 8, 9, 10, 11, 30, 31] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300079 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(NC(=O)C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 195, 201, 201, 201, 201, 201, 150, 96, 150, 152, 40, 13, 56, 56, 13, 13, 1, 13, 1, 1, 1, 56, 56, 201, 201, 201, 201, 201, 201, 96, 56, 56, 13, 1, 1, 1, 1, 1, 56, 56] 201 rigid atoms, others: [37, 38, 39, 40, 41, 20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 753 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300079 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300079 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300079/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300079/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300079 Building REAL300000300080 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300080' /scratch/stefan/7770550/working/building/REAL300000300080 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300080 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300080/0 /scratch/stefan/7770550/working/building/REAL300000300080 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/109 `/scratch/stefan/7770550/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C(Cl)O1) `REAL300000300080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300080 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 9, 9, 9, 51, 51, 1, 1, 53, 53, 53, 53, 1, 1, 9, 51, 51, 51, 51, 51, 1, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300080 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 7, 23, 53, 53, 35, 53, 141, 141, 141, 201, 201, 53, 53, 1, 1, 1, 1, 53, 53, 141, 201, 201, 201, 201, 201, 53, 53] 201 rigid atoms, others: [1, 3, 4, 5, 6, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 672 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300080 none O=C([O-])C1=CC(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 16, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 159, 89, 158, 160, 38, 13, 51, 51, 13, 13, 1, 13, 1, 1, 1, 51, 51, 201, 201, 201, 201, 51, 51, 13, 1, 1, 1, 1, 1, 51, 51] 201 rigid atoms, others: [32, 33, 15, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 669 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300080 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300080 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300080/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300080 Building REAL300000300081 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300081' /scratch/stefan/7770550/working/building/REAL300000300081 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300081 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300081/0 /scratch/stefan/7770550/working/building/REAL300000300081 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/110 `/scratch/stefan/7770550/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1) `REAL300000300081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300081 none CCC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [80, 42, 42, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 8, 41, 41, 1, 1, 42, 42, 42, 42, 42, 42, 80, 80, 80, 80, 80, 1, 1, 8, 41, 41, 41, 41, 41, 1, 1, 42] 201 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 40, 18, 19, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 356 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300081 none CCC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 7, 7, 7, 21, 42, 42, 31, 42, 104, 104, 104, 199, 199, 42, 42, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 42, 42, 104, 199, 199, 199, 199, 199, 42, 42, 1] 201 rigid atoms, others: [1, 2, 3, 4, 41, 20, 21, 22, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 661 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300081 none CCC1=C(S(=O)(=O)[N-]C2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 199, 199, 135, 68, 135, 135, 36, 13, 41, 41, 13, 13, 1, 13, 1, 1, 1, 41, 41, 199, 199, 199, 199, 199, 199, 201, 201, 201, 201, 201, 41, 41, 13, 1, 1, 1, 1, 1, 41, 41, 199] 201 rigid atoms, others: [34, 35, 36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 622 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300081 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300081/1 /scratch/stefan/7770550/working/building/REAL300000300081 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/111 `/scratch/stefan/7770550/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1) `REAL300000300081.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300081 none CCC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [72, 29, 29, 13, 4, 13, 13, 1, 1, 1, 1, 1, 1, 8, 8, 8, 46, 46, 1, 1, 29, 29, 29, 29, 29, 29, 72, 72, 72, 72, 72, 4, 1, 1, 8, 46, 46, 46, 46, 46, 1, 1, 29] 201 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 40, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300081 none CCC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 5, 5, 5, 13, 29, 29, 21, 21, 85, 85, 85, 196, 196, 29, 29, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 13, 29, 29, 85, 196, 196, 196, 196, 196, 29, 29, 1] 201 rigid atoms, others: [1, 2, 3, 4, 42, 20, 21, 22, 23, 24, 25] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300081 none CCC1=C(S(=O)(=O)NC2=CC=C(NC(=O)C3CC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.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, 1, 14, 11, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 196, 196, 146, 77, 146, 146, 38, 27, 46, 46, 13, 13, 1, 13, 1, 1, 1, 46, 46, 195, 195, 195, 195, 196, 196, 201, 201, 201, 201, 201, 77, 46, 46, 13, 1, 1, 1, 1, 1, 46, 46, 195] 201 rigid atoms, others: [35, 36, 37, 38, 39, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 716 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300081 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300081 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300081/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300081/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300081 Building REAL300000300082 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300082' /scratch/stefan/7770550/working/building/REAL300000300082 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300082 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300082/0 /scratch/stefan/7770550/working/building/REAL300000300082 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/112 `/scratch/stefan/7770550/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300082 none COC(=O)C1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 37, 17, 17, 17, 17, 17, 17, 8, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 37, 37, 37, 17, 17, 17, 17, 17, 8, 1, 1, 1, 2, 2, 2, 17] 37 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300082 none COC(=O)C1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 5, 9, 17, 17, 17, 17, 17, 1, 7, 7, 7, 1, 1, 2, 2, 2, 5, 17, 17, 17, 17, 17, 17, 1] 37 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 40, 24, 28, 29] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300082 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300082/1 /scratch/stefan/7770550/working/building/REAL300000300082 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/113 `/scratch/stefan/7770550/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300082.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300082 none COC(=O)C1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 17, 35, 17, 17, 17, 17, 17, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 35, 35, 35, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 35 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300082 none COC(=O)C1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 17, 17, 7, 7, 17, 17, 17, 17, 17, 1, 8, 8, 8, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 17, 1] 35 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 39, 24, 28, 29] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300082 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300082 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300082/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300082/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300082 Building REAL300000300083 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300083' /scratch/stefan/7770550/working/building/REAL300000300083 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300083 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300083/0 /scratch/stefan/7770550/working/building/REAL300000300083 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/114 `/scratch/stefan/7770550/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300083 none COC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 17, 52, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 52, 52, 52, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 52 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300083 none COC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 9, 9, 9, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 52 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 27, 28, 29, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300083 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300083/1 /scratch/stefan/7770550/working/building/REAL300000300083 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/115 `/scratch/stefan/7770550/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300083.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300083 none COC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 17, 47, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 47, 47, 47, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 47 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300083 none COC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 15, 17, 17, 17, 17, 17, 17, 1, 6, 6, 6, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1] 47 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 36, 27, 28, 29] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300083 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300083 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300083/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300083/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300083 Building REAL300000300084 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300084' /scratch/stefan/7770550/working/building/REAL300000300084 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300084 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300084/0 /scratch/stefan/7770550/working/building/REAL300000300084 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/116 `/scratch/stefan/7770550/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCC2=C1) `REAL300000300084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300084 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 15, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300084 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 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 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300084 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300084 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300084/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300084 Building REAL300000300085 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300085' /scratch/stefan/7770550/working/building/REAL300000300085 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300085 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300085/0 /scratch/stefan/7770550/working/building/REAL300000300085 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/117 `/scratch/stefan/7770550/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2CC1) `REAL300000300085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300085 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 26, 34, 39, 39, 39, 39, 26, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300085 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 1, 8, 39, 39, 39, 39, 39, 39, 39, 39, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300085 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300085 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300085/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300085 Building REAL300000300086 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300086' /scratch/stefan/7770550/working/building/REAL300000300086 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300086 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300086/0 /scratch/stefan/7770550/working/building/REAL300000300086 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/118 `/scratch/stefan/7770550/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1F) `REAL300000300086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300086 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 18, 23, 26, 26, 26, 26, 18, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1, 1] 26 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300086 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300086 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300086 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300086/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300086 Building REAL300000300087 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300087' /scratch/stefan/7770550/working/building/REAL300000300087 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300087 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300087/0 /scratch/stefan/7770550/working/building/REAL300000300087 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/119 `/scratch/stefan/7770550/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([O-])C([N+](=O)[O-])=C1) `REAL300000300087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300087 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300087 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300087 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300087 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300087/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300087 Building REAL300000300088 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300088' /scratch/stefan/7770550/working/building/REAL300000300088 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300088 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300088/0 /scratch/stefan/7770550/working/building/REAL300000300088 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/120 `/scratch/stefan/7770550/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1) `REAL300000300088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300088 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300088 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300088 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300088/1 /scratch/stefan/7770550/working/building/REAL300000300088 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/121 `/scratch/stefan/7770550/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)N=C1) `REAL300000300088.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300088 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300088 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300088 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300088 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300088/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300088/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300088 Building REAL300000300089 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300089' /scratch/stefan/7770550/working/building/REAL300000300089 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300089 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300089/0 /scratch/stefan/7770550/working/building/REAL300000300089 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/122 `/scratch/stefan/7770550/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C#N)=C1) `REAL300000300089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300089 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300089 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300089 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300089/1 /scratch/stefan/7770550/working/building/REAL300000300089 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/123 `/scratch/stefan/7770550/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C#N)=C1) `REAL300000300089.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300089 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300089 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300089 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300089 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300089/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300089/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300089 Building REAL300000300090 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300090' /scratch/stefan/7770550/working/building/REAL300000300090 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300090 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300090/0 /scratch/stefan/7770550/working/building/REAL300000300090 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/124 `/scratch/stefan/7770550/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1) `REAL300000300090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300090 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1] 9 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300090 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300090 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300090/1 /scratch/stefan/7770550/working/building/REAL300000300090 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/125 `/scratch/stefan/7770550/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1) `REAL300000300090.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300090 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 9 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300090 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300090 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300090 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300090/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300090/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300090 Building REAL300000300091 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300091' /scratch/stefan/7770550/working/building/REAL300000300091 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300091 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300091/0 /scratch/stefan/7770550/working/building/REAL300000300091 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/126 `/scratch/stefan/7770550/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C=C1F) `REAL300000300091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300091 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 15, 19, 19, 19, 19, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300091 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300091 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300091/1 /scratch/stefan/7770550/working/building/REAL300000300091 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/127 `/scratch/stefan/7770550/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1F) `REAL300000300091.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300091 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300091 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300091 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300091 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300091/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300091/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300091 Building REAL300000300092 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300092' /scratch/stefan/7770550/working/building/REAL300000300092 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300092 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300092/0 /scratch/stefan/7770550/working/building/REAL300000300092 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/128 `/scratch/stefan/7770550/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C=C1C(F)(F)F) `REAL300000300092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300092 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 5, 13, 13, 13, 13, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 1, 1, 1] 13 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300092 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300092 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300092/1 /scratch/stefan/7770550/working/building/REAL300000300092 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/129 `/scratch/stefan/7770550/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1C(F)(F)F) `REAL300000300092.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300092 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300092 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300092 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300092 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300092/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300092/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300092 Building REAL300000300093 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300093' /scratch/stefan/7770550/working/building/REAL300000300093 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300093 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300093/0 /scratch/stefan/7770550/working/building/REAL300000300093 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/130 `/scratch/stefan/7770550/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1Br) `REAL300000300093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300093 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300093 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 33, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300093 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300093 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300093/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300093 Building REAL300000300094 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300094' /scratch/stefan/7770550/working/building/REAL300000300094 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300094 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300094/0 /scratch/stefan/7770550/working/building/REAL300000300094 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/131 `/scratch/stefan/7770550/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(OC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=C1) `REAL300000300094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300094 none CC1=CC=CC(OC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 8, 15, 15, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 15, 15, 15, 15, 8, 15, 15, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1, 15] 161 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 44, 43, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300094 none CC1=CC=CC(OC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 25, 25, 25, 81, 161, 161, 161, 161, 161, 161, 161, 161, 161, 15, 15, 1, 2, 2, 2, 1, 1, 1, 15, 15, 81, 161, 161, 161, 161, 161, 161, 15, 15, 1] 161 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 33, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300094 none CC1=CC=CC(OC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 161, 161, 65, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 161, 161, 161, 161, 161, 161, 161, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 161] 161 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 281 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300094 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300094 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300094/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300094 Building REAL300000300095 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300095' /scratch/stefan/7770550/working/building/REAL300000300095 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300095 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300095/0 /scratch/stefan/7770550/working/building/REAL300000300095 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/132 `/scratch/stefan/7770550/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1Br) `REAL300000300095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300095 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1] 11 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300095 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300095 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300095/1 /scratch/stefan/7770550/working/building/REAL300000300095 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/133 `/scratch/stefan/7770550/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1Br) `REAL300000300095.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300095 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 5, 5, 12, 12, 12, 12, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 12 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300095 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 12, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300095 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300095 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300095/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300095/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300095 Building REAL300000300096 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300096' /scratch/stefan/7770550/working/building/REAL300000300096 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300096 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300096/0 /scratch/stefan/7770550/working/building/REAL300000300096 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/134 `/scratch/stefan/7770550/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1NC(C)=O) `REAL300000300096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300096 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1NC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 1, 5, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [39, 23, 23, 23, 23, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 49, 49, 49, 39, 39, 39, 23, 23, 7, 1, 1, 1, 2, 2, 2, 23, 49, 49, 49, 49] 49 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300096 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1NC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 1, 5, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 13, 17, 23, 23, 23, 23, 23, 1, 1, 1, 4, 4, 4, 3, 3, 3, 1, 1, 9, 23, 23, 23, 23, 23, 23, 1, 4, 4, 4, 4] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300096 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300096 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300096/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300096 Building REAL300000300097 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300097' /scratch/stefan/7770550/working/building/REAL300000300097 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300097 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300097/0 /scratch/stefan/7770550/working/building/REAL300000300097 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/135 `/scratch/stefan/7770550/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)(F)F)C=C1) `REAL300000300097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300097 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1] 49 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300097 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 49, 49, 49, 49, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300097 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300097 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300097/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300097 Building REAL300000300098 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300098' /scratch/stefan/7770550/working/building/REAL300000300098 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300098 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300098/0 /scratch/stefan/7770550/working/building/REAL300000300098 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/136 `/scratch/stefan/7770550/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000300098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300098 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 6, 6, 6, 1, 1] 39 rigid atoms, others: [34, 35, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300098 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 39, 39, 39, 9, 9] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300098 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300098/1 /scratch/stefan/7770550/working/building/REAL300000300098 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/137 `/scratch/stefan/7770550/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1) `REAL300000300098.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300098 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 6, 6, 6, 1, 1] 39 rigid atoms, others: [33, 34, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300098 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)NCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 39, 39, 39, 9, 9] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300098 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300098 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300098/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300098/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300098 Building REAL300000300099 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300099' /scratch/stefan/7770550/working/building/REAL300000300099 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300099 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300099/0 /scratch/stefan/7770550/working/building/REAL300000300099 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/138 `/scratch/stefan/7770550/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1) `REAL300000300099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300099 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 5, 9, 12, 12, 12, 12, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1] 12 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300099 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 5, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300099 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300099 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300099/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300099 Building REAL300000300100 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300100' /scratch/stefan/7770550/working/building/REAL300000300100 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300100 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300100/0 /scratch/stefan/7770550/working/building/REAL300000300100 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/139 `/scratch/stefan/7770550/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C(C)=C(C)C(C)=C1C) `REAL300000300100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300100 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C(C)=C(C)C(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 84 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300100 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C(C)=C(C)C(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 5, 1, 5, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 64 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300100 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300100 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300100/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300100 Building REAL300000300101 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300101' /scratch/stefan/7770550/working/building/REAL300000300101 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300101 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300101/0 /scratch/stefan/7770550/working/building/REAL300000300101 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/140 `/scratch/stefan/7770550/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCCOC2=C1) `REAL300000300101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300101 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 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, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300101 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 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, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300101 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300101 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300101/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300101 Building REAL300000300102 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300102' /scratch/stefan/7770550/working/building/REAL300000300102 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300102 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300102/0 /scratch/stefan/7770550/working/building/REAL300000300102 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/141 `/scratch/stefan/7770550/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-]) `REAL300000300102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300102 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300102 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 36, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300102 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300102/1 /scratch/stefan/7770550/working/building/REAL300000300102 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/142 `/scratch/stefan/7770550/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-]) `REAL300000300102.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300102 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300102 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 19, 20, 21, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300102 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300102 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300102/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300102/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300102 Building REAL300000300103 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300103' /scratch/stefan/7770550/working/building/REAL300000300103 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300103 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300103/0 /scratch/stefan/7770550/working/building/REAL300000300103 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/143 `/scratch/stefan/7770550/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300103 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 2, 2, 2] 7 rigid atoms, others: [35, 36, 37, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 20 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300103 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 1, 1, 1, 5, 5, 5, 5, 7, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 3, 1, 1, 3, 3, 1, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 34, 13, 30, 31] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300103 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300103/1 /scratch/stefan/7770550/working/building/REAL300000300103 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/144 `/scratch/stefan/7770550/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300103.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300103 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 9, 5, 1, 1, 1, 2, 2, 2] 13 rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 41 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300103 none COC1=CC=C(C=CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 5, 5, 1, 5, 9, 9, 9, 9, 9, 9] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 11, 12, 34, 13, 30, 31] set([7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300103 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300103 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300103/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300103/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300103 Building REAL300000300104 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300104' /scratch/stefan/7770550/working/building/REAL300000300104 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300104 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300104/0 /scratch/stefan/7770550/working/building/REAL300000300104 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/145 `/scratch/stefan/7770550/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)S1) `REAL300000300104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300104 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 21, 21, 21, 21, 21, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300104 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 23, 24, 25] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300104 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300104 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300104/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300104 Building REAL300000300105 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300105' /scratch/stefan/7770550/working/building/REAL300000300105 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300105 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300105/0 /scratch/stefan/7770550/working/building/REAL300000300105 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/146 `/scratch/stefan/7770550/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C(Cl)=CC(C)=C1Cl) `REAL300000300105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300105 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C(Cl)=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 16, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 20, 34, 34, 34, 34, 34, 20, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 2, 2, 2, 1, 2, 2, 2] 34 rigid atoms, others: [33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300105 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C(Cl)=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 16, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 34, 34, 34, 34, 23, 34, 34, 34, 34, 2, 2, 2, 1, 1, 1, 34, 34, 34, 23, 34, 34, 34] 34 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300105 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300105/1 /scratch/stefan/7770550/working/building/REAL300000300105 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/147 `/scratch/stefan/7770550/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C(Cl)=CC(C)=C1Cl) `REAL300000300105.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300105 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C(Cl)=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 16, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 19, 29, 29, 29, 29, 29, 19, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 19, 2, 2, 2, 1, 2, 2, 2] 29 rigid atoms, others: [34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300105 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C(Cl)=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 16, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 29, 29, 29, 29, 19, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 5, 29, 29, 29, 19, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300105 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300105 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300105/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300105/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300105 Building REAL300000300106 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300106' /scratch/stefan/7770550/working/building/REAL300000300106 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300106 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300106/0 /scratch/stefan/7770550/working/building/REAL300000300106 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/148 `/scratch/stefan/7770550/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(C(C)(C)C)C=C1C) `REAL300000300106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300106 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(C(C)(C)C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 12, 18, 24, 24, 24, 24, 12, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 24, 24, 24, 24, 24, 24, 12, 2, 2, 2, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2] 24 rigid atoms, others: [36, 11, 14, 15, 16, 17, 18, 19, 46, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300106 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(C(C)(C)C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 24, 24, 24, 16, 16, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300106 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300106 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300106/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300106 Building REAL300000300107 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300107' /scratch/stefan/7770550/working/building/REAL300000300107 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300107 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300107/0 /scratch/stefan/7770550/working/building/REAL300000300107 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/149 `/scratch/stefan/7770550/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2CCCCC2)C=C1) `REAL300000300107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300107 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 41 rigid atoms, others: [33, 34, 11, 14, 15, 16, 17, 18, 46, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300107 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 41, 41, 41, 41, 41, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 9, 9] 41 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300107 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2CCCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 21, 41, 41, 41, 41, 41, 21, 7, 6, 7, 7, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 41, 41, 41, 41, 41, 41, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 41 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 46, 47]) total number of confs: 206 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300107 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300107 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300107/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300107 Building REAL300000300108 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300108' /scratch/stefan/7770550/working/building/REAL300000300108 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300108 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300108/0 /scratch/stefan/7770550/working/building/REAL300000300108 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/150 `/scratch/stefan/7770550/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1) `REAL300000300108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300108 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1] 9 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300108 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300108 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300108 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300108/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300108 Building REAL300000300109 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300109' /scratch/stefan/7770550/working/building/REAL300000300109 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300109 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300109/0 /scratch/stefan/7770550/working/building/REAL300000300109 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/151 `/scratch/stefan/7770550/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCCCC2=C1) `REAL300000300109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300109 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 10, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300109 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300109 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300109 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300109/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300109 Building REAL300000300110 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300110' /scratch/stefan/7770550/working/building/REAL300000300110 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300110 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300110/0 /scratch/stefan/7770550/working/building/REAL300000300110 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/152 `/scratch/stefan/7770550/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1) `REAL300000300110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300110 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1] 9 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300110 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300110 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300110 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300110/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300110 Building REAL300000300111 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300111' /scratch/stefan/7770550/working/building/REAL300000300111 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300111 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300111/0 /scratch/stefan/7770550/working/building/REAL300000300111 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/153 `/scratch/stefan/7770550/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300111 none COC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 39, 39, 39, 39, 39, 39, 41, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 39, 41, 41, 41, 39, 39, 41, 41, 41, 1, 1, 1, 2, 2, 2, 39] 41 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300111 none COC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 21, 39, 39, 21, 21, 39, 39, 39, 39, 39, 1, 2, 2, 2, 1, 1, 4, 4, 4, 39, 39, 39, 39, 39, 39, 1] 41 rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9, 38, 23, 27, 28] set([0, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300111 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300111/1 /scratch/stefan/7770550/working/building/REAL300000300111 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/154 `/scratch/stefan/7770550/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300111.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300111 none COC1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 51, 51, 51, 51, 51, 51, 58, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 58, 58, 58, 51, 51, 58, 58, 58, 7, 1, 1, 1, 2, 2, 2, 51] 58 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300111 none COC1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 23, 51, 51, 23, 41, 51, 51, 51, 51, 51, 1, 3, 3, 3, 1, 1, 3, 3, 3, 23, 51, 51, 51, 51, 51, 51, 1] 58 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 8, 9, 23, 27, 28] set([0, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300111 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300111 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300111/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300111/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300111 Building REAL300000300112 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300112' /scratch/stefan/7770550/working/building/REAL300000300112 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300112 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300112/0 /scratch/stefan/7770550/working/building/REAL300000300112 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/155 `/scratch/stefan/7770550/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC) `REAL300000300112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300112 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 23, 23, 23, 23, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 40, 40, 40, 40, 23, 23, 5, 1, 1, 1, 2, 2, 2, 23, 40, 40, 40] 40 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300112 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 17, 17, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 3, 3, 1, 1, 9, 23, 23, 23, 23, 23, 23, 1, 3, 3, 3] 40 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300112 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300112 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300112/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300112 Building REAL300000300113 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300113' /scratch/stefan/7770550/working/building/REAL300000300113 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300113 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300113/0 /scratch/stefan/7770550/working/building/REAL300000300113 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/156 `/scratch/stefan/7770550/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCCC2=C1) `REAL300000300113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300113 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300113 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300113 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300113 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300113/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300113 Building REAL300000300114 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300114' /scratch/stefan/7770550/working/building/REAL300000300114 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300114 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300114/0 /scratch/stefan/7770550/working/building/REAL300000300114 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/157 `/scratch/stefan/7770550/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300114 none CC1=NOC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 1, 1, 1, 2, 2, 2] 34 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 100 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300114 none CC1=NOC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 21, 34, 34, 28, 34, 34, 34, 34, 34, 34, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300114 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300114 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300114/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300114 Building REAL300000300115 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300115' /scratch/stefan/7770550/working/building/REAL300000300115 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300115 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300115/0 /scratch/stefan/7770550/working/building/REAL300000300115 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/158 `/scratch/stefan/7770550/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(Cl)=C1) `REAL300000300115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300115 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300115 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300115 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300115/1 /scratch/stefan/7770550/working/building/REAL300000300115 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/159 `/scratch/stefan/7770550/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(Cl)=C1) `REAL300000300115.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300115 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 16, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300115 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300115 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300115 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300115/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300115/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300115 Building REAL300000300116 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300116' /scratch/stefan/7770550/working/building/REAL300000300116 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300116 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300116/0 /scratch/stefan/7770550/working/building/REAL300000300116 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/160 `/scratch/stefan/7770550/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1) `REAL300000300116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300116 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1] 9 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300116 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300116 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300116 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300116/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300116 Building REAL300000300117 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300117' /scratch/stefan/7770550/working/building/REAL300000300117 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300117 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300117/0 /scratch/stefan/7770550/working/building/REAL300000300117 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/161 `/scratch/stefan/7770550/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(F)=C1) `REAL300000300117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300117 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300117 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300117 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300117/1 /scratch/stefan/7770550/working/building/REAL300000300117 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/162 `/scratch/stefan/7770550/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(F)=C1) `REAL300000300117.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300117 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300117 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300117 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300117 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300117/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300117/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300117 Building REAL300000300118 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300118' /scratch/stefan/7770550/working/building/REAL300000300118 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300118 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300118/0 /scratch/stefan/7770550/working/building/REAL300000300118 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/163 `/scratch/stefan/7770550/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1Cl) `REAL300000300118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300118 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 13, 17, 17, 17, 17, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300118 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300118 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300118/1 /scratch/stefan/7770550/working/building/REAL300000300118 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/164 `/scratch/stefan/7770550/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC=C1Cl) `REAL300000300118.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300118 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 11, 15, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1] 15 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300118 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300118 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300118 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300118/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300118/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300118 Building REAL300000300119 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300119' /scratch/stefan/7770550/working/building/REAL300000300119 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300119 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300119/0 /scratch/stefan/7770550/working/building/REAL300000300119 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/165 `/scratch/stefan/7770550/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(F)(F)F)=C1) `REAL300000300119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300119 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300119 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300119 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300119/1 /scratch/stefan/7770550/working/building/REAL300000300119 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/166 `/scratch/stefan/7770550/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(F)(F)F)=C1) `REAL300000300119.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300119 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300119 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 13, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300119 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300119 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300119/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300119/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300119 Building REAL300000300120 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300120' /scratch/stefan/7770550/working/building/REAL300000300120 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300120 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300120/0 /scratch/stefan/7770550/working/building/REAL300000300120 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/167 `/scratch/stefan/7770550/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300120 none CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 34, 33, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300120 none CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 20, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300120 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300120 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300120/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300120 Building REAL300000300121 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300121' /scratch/stefan/7770550/working/building/REAL300000300121 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300121 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300121/0 /scratch/stefan/7770550/working/building/REAL300000300121 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/168 `/scratch/stefan/7770550/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C=CC1=CC=CC=C1) `REAL300000300121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300121 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C=CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 58, 74, 74, 74, 74, 74, 58, 35, 6, 35, 35, 6, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 74, 58, 6, 6, 1, 1, 1, 1, 1] 74 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 301 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300121 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C=CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 57, 57, 74, 74, 69, 74, 74, 2, 2, 2, 1, 1, 1, 8, 57, 57, 74, 74, 74, 74, 74] 74 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 244 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300121 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300121 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300121/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300121 Building REAL300000300122 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300122' /scratch/stefan/7770550/working/building/REAL300000300122 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300122 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300122/0 /scratch/stefan/7770550/working/building/REAL300000300122 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/169 `/scratch/stefan/7770550/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C(F)(F)F) `REAL300000300122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300122 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 5, 6, 12, 12, 12, 12, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1] 12 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300122 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 12, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300122 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300122/1 /scratch/stefan/7770550/working/building/REAL300000300122 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/170 `/scratch/stefan/7770550/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C(F)(F)F) `REAL300000300122.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300122 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300122 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300122 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300122 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300122/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300122/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300122 Building REAL300000300123 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300123' /scratch/stefan/7770550/working/building/REAL300000300123 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300123 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300123/0 /scratch/stefan/7770550/working/building/REAL300000300123 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/171 `/scratch/stefan/7770550/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(C(F)(F)F)=C1) `REAL300000300123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300123 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300123 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300123 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300123/1 /scratch/stefan/7770550/working/building/REAL300000300123 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/172 `/scratch/stefan/7770550/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C(F)(F)F)=C1) `REAL300000300123.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300123 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300123 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300123 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300123 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300123/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300123/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300123 Building REAL300000300124 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300124' /scratch/stefan/7770550/working/building/REAL300000300124 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300124 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300124/0 /scratch/stefan/7770550/working/building/REAL300000300124 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/173 `/scratch/stefan/7770550/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Cl)=C1) `REAL300000300124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300124 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300124 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300124 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300124/1 /scratch/stefan/7770550/working/building/REAL300000300124 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/174 `/scratch/stefan/7770550/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Cl)=C1) `REAL300000300124.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300124 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300124 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300124 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300124 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300124/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300124/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300124 Building REAL300000300125 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300125' /scratch/stefan/7770550/working/building/REAL300000300125 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300125 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300125/0 /scratch/stefan/7770550/working/building/REAL300000300125 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/175 `/scratch/stefan/7770550/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=CC=C1Cl) `REAL300000300125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300125 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 13, 17, 17, 17, 17, 9, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300125 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 17, 17, 17, 17, 17, 17, 15, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300125 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300125/1 /scratch/stefan/7770550/working/building/REAL300000300125 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/176 `/scratch/stefan/7770550/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(F)(F)F)=CC=C1Cl) `REAL300000300125.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300125 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(F)(F)F)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 15, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300125 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(F)(F)F)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300125 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300125 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300125/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300125/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300125 Building REAL300000300126 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300126' /scratch/stefan/7770550/working/building/REAL300000300126 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300126 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300126/0 /scratch/stefan/7770550/working/building/REAL300000300126 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/177 `/scratch/stefan/7770550/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300126 none CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 29, 21, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 29, 29, 29, 21, 21, 7, 1, 1, 1, 2, 2, 2, 21, 21] 29 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300126 none CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 14, 17, 21, 21, 21, 21, 21, 1, 1, 4, 4, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1, 1] 29 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 36, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300126 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300126/1 /scratch/stefan/7770550/working/building/REAL300000300126 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/178 `/scratch/stefan/7770550/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300126.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300126 none CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 27, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 27, 27, 27, 19, 19, 1, 1, 1, 2, 2, 2, 19, 19] 27 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300126 none CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 1, 4, 4, 4, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1] 27 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 35, 21, 22, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300126 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300126 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300126/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300126/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300126 Building REAL300000300127 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300127' /scratch/stefan/7770550/working/building/REAL300000300127 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300127 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300127/0 /scratch/stefan/7770550/working/building/REAL300000300127 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/179 `/scratch/stefan/7770550/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300127 none CC1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 1, 1, 2, 2, 2, 13] 13 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300127 none CC1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 5, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 1, 1, 2, 2, 2, 5, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 25, 26, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300127 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300127 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300127/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300127 Building REAL300000300128 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300128' /scratch/stefan/7770550/working/building/REAL300000300128 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300128 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300128/0 /scratch/stefan/7770550/working/building/REAL300000300128 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/180 `/scratch/stefan/7770550/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300128 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300128 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300128 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300128 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300128/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300128 Building REAL300000300129 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300129' /scratch/stefan/7770550/working/building/REAL300000300129 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300129 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300129/0 /scratch/stefan/7770550/working/building/REAL300000300129 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/181 `/scratch/stefan/7770550/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(Cl)=C1) `REAL300000300129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300129 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300129 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300129 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300129 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300129/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300129 Building REAL300000300130 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300130' /scratch/stefan/7770550/working/building/REAL300000300130 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300130 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300130/0 /scratch/stefan/7770550/working/building/REAL300000300130 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/182 `/scratch/stefan/7770550/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300130 none CC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 18, 41, 18, 18, 18, 18, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 41, 41, 41, 18, 18, 18, 5, 1, 1, 1, 2, 2, 2, 18] 41 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300130 none CC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 18, 9, 17, 18, 18, 18, 18, 18, 1, 7, 7, 7, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 1] 41 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 22, 36, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300130 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300130/1 /scratch/stefan/7770550/working/building/REAL300000300130 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/183 `/scratch/stefan/7770550/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300130.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300130 none CC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 26, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 26, 26, 26, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 26 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300130 none CC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 14, 17, 17, 17, 17, 17, 17, 1, 7, 7, 7, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1] 26 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 35, 22, 26, 27, 28] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300130 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300130 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300130/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300130/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300130 Building REAL300000300131 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300131' /scratch/stefan/7770550/working/building/REAL300000300131 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300131 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300131/0 /scratch/stefan/7770550/working/building/REAL300000300131 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/184 `/scratch/stefan/7770550/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1) `REAL300000300131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300131 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 19, 19, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 8, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19] 19 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300131 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 19, 19, 13, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 1, 1, 11, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 25, 26, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300131 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300131 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300131/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300131 Building REAL300000300132 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300132' /scratch/stefan/7770550/working/building/REAL300000300132 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300132 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300132/0 /scratch/stefan/7770550/working/building/REAL300000300132 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/185 `/scratch/stefan/7770550/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300132 none COC(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 29, 45, 29, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 45, 45, 45, 29, 29, 29, 29, 1, 1, 1, 2, 2, 2] 45 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300132 none COC(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 29, 29, 15, 15, 29, 29, 29, 29, 29, 5, 5, 5, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29] 45 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300132 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300132/1 /scratch/stefan/7770550/working/building/REAL300000300132 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/186 `/scratch/stefan/7770550/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300132.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300132 none COC(=O)C1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 35, 19, 19, 13, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 19, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300132 none COC(=O)C1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 9, 19, 19, 19, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300132 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300132 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300132/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300132/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300132 Building REAL300000300133 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300133' /scratch/stefan/7770550/working/building/REAL300000300133 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300133 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300133/0 /scratch/stefan/7770550/working/building/REAL300000300133 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/187 `/scratch/stefan/7770550/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300133 none CCOC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 53, 17, 53, 9, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 67, 67, 67, 67, 67, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 67 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300133 none CCOC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 12, 12, 12, 11, 11, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 67 rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 40, 23, 24, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300133 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300133/1 /scratch/stefan/7770550/working/building/REAL300000300133 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/188 `/scratch/stefan/7770550/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300133.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300133 none CCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 53, 17, 53, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 65, 65, 65, 65, 65, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17] 65 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300133 none CCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 12, 12, 12, 11, 11, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1] 65 rigid atoms, others: [3, 5, 6, 7, 8, 9, 39, 23, 24, 38, 30, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300133 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300133 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300133/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300133/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300133 Building REAL300000300134 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300134' /scratch/stefan/7770550/working/building/REAL300000300134 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300134 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300134/0 /scratch/stefan/7770550/working/building/REAL300000300134 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/189 `/scratch/stefan/7770550/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Cl)=C1Cl) `REAL300000300134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300134 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 7, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300134 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300134 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300134/1 /scratch/stefan/7770550/working/building/REAL300000300134 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/190 `/scratch/stefan/7770550/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Cl)=C1Cl) `REAL300000300134.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300134 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 7, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300134 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300134 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300134 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300134/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300134/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300134 Building REAL300000300135 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300135' /scratch/stefan/7770550/working/building/REAL300000300135 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300135 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300135/0 /scratch/stefan/7770550/working/building/REAL300000300135 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/191 `/scratch/stefan/7770550/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-]) `REAL300000300135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300135 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 19, 21, 21, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300135 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 3, 3, 3, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300135 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300135/1 /scratch/stefan/7770550/working/building/REAL300000300135 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/192 `/scratch/stefan/7770550/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-]) `REAL300000300135.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300135 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2, 23] 23 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300135 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 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: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 11, 17, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 3, 3, 3, 1, 1, 23, 23, 23, 23, 23, 23, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 36, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300135 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300135 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300135/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300135/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300135 Building REAL300000300136 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300136' /scratch/stefan/7770550/working/building/REAL300000300136 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300136 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300136/0 /scratch/stefan/7770550/working/building/REAL300000300136 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/193 `/scratch/stefan/7770550/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(C)(C)C)C=C1) `REAL300000300136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300136 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 8, 9, 11, 11, 11, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 15 rigid atoms, others: [32, 43, 42, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300136 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 11, 11, 2, 2, 2, 1, 1, 1, 5, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300136 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300136 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300136/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300136 Building REAL300000300137 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300137' /scratch/stefan/7770550/working/building/REAL300000300137 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300137 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300137/0 /scratch/stefan/7770550/working/building/REAL300000300137 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/194 `/scratch/stefan/7770550/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(C)C)C=C1) `REAL300000300137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300137 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 9, 13, 13, 13, 13, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 5, 1, 1, 3, 4, 4, 4, 3, 3, 3, 1, 1] 17 rigid atoms, others: [39, 40, 11, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300137 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 13, 17, 17, 13, 13, 2, 2, 2, 1, 1, 1, 5, 13, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300137 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300137 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300137/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300137 Building REAL300000300138 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300138' /scratch/stefan/7770550/working/building/REAL300000300138 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300138 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300138/0 /scratch/stefan/7770550/working/building/REAL300000300138 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/195 `/scratch/stefan/7770550/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300138 none CCC(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 37, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 37 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300138 none CCC(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 15, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 37 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 42, 43, 34, 22, 23] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300138 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300138 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300138/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300138 Building REAL300000300139 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300139' /scratch/stefan/7770550/working/building/REAL300000300139 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300139 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300139/0 /scratch/stefan/7770550/working/building/REAL300000300139 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/196 `/scratch/stefan/7770550/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(=O)(=O)N(C)C)C=C1) `REAL300000300139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300139 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(=O)(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 37 rigid atoms, others: [33, 34, 41, 42, 11, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300139 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(=O)(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 37, 37, 37, 37, 37, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 37, 37, 37, 37, 37, 37, 9, 9] 37 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300139 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300139/1 /scratch/stefan/7770550/working/building/REAL300000300139 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/197 `/scratch/stefan/7770550/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(=O)(=O)N(C)C)C=C1) `REAL300000300139.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300139 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(=O)(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 35 rigid atoms, others: [32, 33, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300139 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(=O)(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 35, 35, 35, 35, 35, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 35, 35, 35, 35, 35, 35, 9, 9] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300139 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300139 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300139/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300139/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300139 Building REAL300000300140 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300140' /scratch/stefan/7770550/working/building/REAL300000300140 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300140 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300140/0 /scratch/stefan/7770550/working/building/REAL300000300140 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/198 `/scratch/stefan/7770550/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300140 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300140 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 15, 27, 27, 15, 15, 27, 27, 27, 27, 27, 3, 3, 3, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 9, 10, 11, 28, 29, 30] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300140 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300140/1 /scratch/stefan/7770550/working/building/REAL300000300140 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/199 `/scratch/stefan/7770550/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300140.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300140 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 5, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 5, 1, 1, 1, 2, 2, 2] 30 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300140 none COC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 30, 30, 24, 24, 30, 30, 30, 30, 30, 3, 3, 3, 1, 1, 1, 15, 30, 30, 30, 30, 30, 30] 30 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300140 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300140 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300140/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300140/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300140 Building REAL300000300141 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300141' /scratch/stefan/7770550/working/building/REAL300000300141 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300141 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300141/0 /scratch/stefan/7770550/working/building/REAL300000300141 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/200 `/scratch/stefan/7770550/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1) `REAL300000300141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300141 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 13, 5, 9, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 1, 1, 13, 13, 13, 13, 13, 13, 5, 1, 1, 5, 5, 1, 1] 23 rigid atoms, others: [32, 33, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 81 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300141 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 13, 13, 2, 2, 2, 1, 1, 1, 5, 13, 13, 23, 23, 13, 13] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300141 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300141 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300141/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300141 Building REAL300000300142 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300142' /scratch/stefan/7770550/working/building/REAL300000300142 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300142 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300142/0 /scratch/stefan/7770550/working/building/REAL300000300142 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/201 `/scratch/stefan/7770550/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC=C1Cl) `REAL300000300142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300142 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 15, 17, 17, 17, 17, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300142 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300142 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300142 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300142/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300142 Building REAL300000300143 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300143' /scratch/stefan/7770550/working/building/REAL300000300143 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300143 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300143/0 /scratch/stefan/7770550/working/building/REAL300000300143 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/202 `/scratch/stefan/7770550/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)S1) `REAL300000300143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300143 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 21, 21, 21, 21, 21, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300143 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 23, 24, 25] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300143 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300143 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300143/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300143 Building REAL300000300144 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300144' /scratch/stefan/7770550/working/building/REAL300000300144 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300144 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300144/0 /scratch/stefan/7770550/working/building/REAL300000300144 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/203 `/scratch/stefan/7770550/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300144 none CCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 31, 31, 31, 31, 31, 23, 23, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 31 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300144 none CCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 6, 6, 4, 4, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 31 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 39, 21, 22, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300144 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300144 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300144/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300144 Building REAL300000300145 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300145' /scratch/stefan/7770550/working/building/REAL300000300145 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300145 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300145/0 /scratch/stefan/7770550/working/building/REAL300000300145 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/204 `/scratch/stefan/7770550/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300145 none COC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 41, 41, 27, 41, 41, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 47, 47, 47, 41, 41, 41, 41, 1, 1, 1, 2, 2, 2] 47 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300145 none COC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 41, 41, 25, 28, 41, 41, 41, 41, 41, 4, 4, 4, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41] 47 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300145 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300145/1 /scratch/stefan/7770550/working/building/REAL300000300145 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/205 `/scratch/stefan/7770550/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300145.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300145/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300145 none COC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 35, 35, 21, 35, 35, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 35, 35, 35, 35, 5, 1, 1, 1, 2, 2, 2] 37 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300145 none COC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 35, 35, 19, 31, 35, 35, 35, 35, 35, 4, 4, 4, 1, 1, 1, 1, 19, 35, 35, 35, 35, 35, 35] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300145 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300145 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300145/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300145/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300145 Building REAL300000300146 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300146' /scratch/stefan/7770550/working/building/REAL300000300146 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300146 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300146/0 /scratch/stefan/7770550/working/building/REAL300000300146 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/206 `/scratch/stefan/7770550/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-]) `REAL300000300146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300146 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 2, 2, 2, 13] 13 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300146 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 13, 13, 5, 9, 13, 13, 13, 13, 13, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 5, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 36, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300146 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300146 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300146/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300146 Building REAL300000300147 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300147' /scratch/stefan/7770550/working/building/REAL300000300147 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300147 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300147/0 /scratch/stefan/7770550/working/building/REAL300000300147 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/207 `/scratch/stefan/7770550/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300147 none COC1=CC=C(NC(C)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [41, 39, 39, 39, 39, 39, 39, 81, 81, 81, 39, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 41, 41, 41, 39, 39, 81, 81, 81, 81, 39, 1, 1, 1, 2, 2, 2] 81 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300147 none COC1=CC=C(NC(C)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 7, 7, 7, 21, 39, 39, 21, 21, 39, 39, 39, 39, 39, 4, 4, 4, 1, 1, 4, 4, 4, 4, 1, 39, 39, 39, 39, 39, 39] 81 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300147 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300147/1 /scratch/stefan/7770550/working/building/REAL300000300147 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/208 `/scratch/stefan/7770550/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(NC(C)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300147.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300147 none COC1=CC=C(NC(C)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 70, 70, 70, 32, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 70, 70, 70, 70, 32, 7, 1, 1, 1, 2, 2, 2] 70 rigid atoms, others: [37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300147 none COC1=CC=C(NC(C)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 7, 7, 7, 19, 32, 32, 22, 28, 32, 32, 32, 32, 32, 3, 3, 3, 1, 1, 5, 5, 5, 5, 1, 19, 32, 32, 32, 32, 32, 32] 70 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 35, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300147 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300147 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300147/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300147/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300147 Building REAL300000300148 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300148' /scratch/stefan/7770550/working/building/REAL300000300148 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300148 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300148/0 /scratch/stefan/7770550/working/building/REAL300000300148 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/209 `/scratch/stefan/7770550/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(F)=C1F) `REAL300000300148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300148 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 23, 27, 27, 27, 27, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300148 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300148 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300148 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300148/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300148 Building REAL300000300149 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300149' /scratch/stefan/7770550/working/building/REAL300000300149 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300149 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300149/0 /scratch/stefan/7770550/working/building/REAL300000300149 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/210 `/scratch/stefan/7770550/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1) `REAL300000300149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300149 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 7, 7, 9, 9, 9, 9, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 7, 1, 1, 1] 9 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300149 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300149 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300149/1 /scratch/stefan/7770550/working/building/REAL300000300149 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/211 `/scratch/stefan/7770550/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1) `REAL300000300149.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300149 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1] 9 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300149 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300149 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300149 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300149/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300149/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300149 Building REAL300000300150 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300150' /scratch/stefan/7770550/working/building/REAL300000300150 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300150 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300150/0 /scratch/stefan/7770550/working/building/REAL300000300150 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/212 `/scratch/stefan/7770550/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1Cl) `REAL300000300150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300150 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 12, 15, 15, 15, 15, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 15 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300150 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 11, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 13, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300150 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300150/1 /scratch/stefan/7770550/working/building/REAL300000300150 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/213 `/scratch/stefan/7770550/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1Cl) `REAL300000300150.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300150 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 15, 15, 15, 15, 15, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 1, 1, 1, 1] 15 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300150 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 13, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 13, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300150 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300150 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300150/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300150/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300150 Building REAL300000300151 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300151' /scratch/stefan/7770550/working/building/REAL300000300151 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300151 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300151/0 /scratch/stefan/7770550/working/building/REAL300000300151 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/214 `/scratch/stefan/7770550/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Br)=C1) `REAL300000300151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300151 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300151 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300151 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300151/1 /scratch/stefan/7770550/working/building/REAL300000300151 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/215 `/scratch/stefan/7770550/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Br)=C1) `REAL300000300151.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300151 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 13, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300151 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300151 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300151 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300151/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300151/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300151 Building REAL300000300152 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300152' /scratch/stefan/7770550/working/building/REAL300000300152 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300152 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300152/0 /scratch/stefan/7770550/working/building/REAL300000300152 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/216 `/scratch/stefan/7770550/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1) `REAL300000300152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300152 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300152 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300152 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300152/1 /scratch/stefan/7770550/working/building/REAL300000300152 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/217 `/scratch/stefan/7770550/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1) `REAL300000300152.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300152 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 13, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300152 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300152 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300152 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300152/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300152/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300152 Building REAL300000300153 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300153' /scratch/stefan/7770550/working/building/REAL300000300153 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300153 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300153/0 /scratch/stefan/7770550/working/building/REAL300000300153 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/218 `/scratch/stefan/7770550/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300153 none CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300153 none CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 19, 19, 15, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 11, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300153 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300153/1 /scratch/stefan/7770550/working/building/REAL300000300153 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/219 `/scratch/stefan/7770550/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300153.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300153 none CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 15, 27, 27, 27, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 27, 27, 27, 27, 15, 27, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300153 none CC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 27, 27, 19, 21, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300153 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300153 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300153/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300153/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300153 Building REAL300000300154 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300154' /scratch/stefan/7770550/working/building/REAL300000300154 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300154 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300154/0 /scratch/stefan/7770550/working/building/REAL300000300154 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/220 `/scratch/stefan/7770550/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C([N+](=O)[O-])=C1) `REAL300000300154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300154 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300154 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300154 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300154/1 /scratch/stefan/7770550/working/building/REAL300000300154 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/221 `/scratch/stefan/7770550/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C([N+](=O)[O-])=C1) `REAL300000300154.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300154/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300154 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300154 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300154 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300154 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300154/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300154/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300154 Building REAL300000300155 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300155' /scratch/stefan/7770550/working/building/REAL300000300155 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300155 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300155/0 /scratch/stefan/7770550/working/building/REAL300000300155 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/222 `/scratch/stefan/7770550/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300155 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 2, 2, 2, 13, 13] 13 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300155 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 11, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 1, 1, 9, 13, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 20, 21, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300155 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300155 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300155/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300155 Building REAL300000300156 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300156' /scratch/stefan/7770550/working/building/REAL300000300156 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300156 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300156/0 /scratch/stefan/7770550/working/building/REAL300000300156 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/223 `/scratch/stefan/7770550/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1[N+](=O)[O-]) `REAL300000300156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300156 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 5, 7, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 11 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300156 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300156 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300156 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300156/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300156 Building REAL300000300157 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300157' /scratch/stefan/7770550/working/building/REAL300000300157 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300157 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300157/0 /scratch/stefan/7770550/working/building/REAL300000300157 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/224 `/scratch/stefan/7770550/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300157 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 2, 2, 2, 9, 9] 9 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300157 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 8, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 1, 1, 5, 9, 9, 9, 9, 9, 9, 1, 1] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 19, 20, 24, 25, 33] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300157 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300157 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300157/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300157 Building REAL300000300158 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300158' /scratch/stefan/7770550/working/building/REAL300000300158 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300158 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300158/0 /scratch/stefan/7770550/working/building/REAL300000300158 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/225 `/scratch/stefan/7770550/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300158 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 27, 15, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 27, 27, 39, 39, 39, 39, 39, 27, 27, 7, 1, 1, 1, 2, 2, 2, 27, 27] 39 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 169 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300158 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 9, 17, 27, 27, 27, 27, 27, 1, 1, 5, 5, 5, 5, 5, 1, 1, 9, 27, 27, 27, 27, 27, 27, 1, 1] 39 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 22, 38, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300158 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300158 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300158/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300158 Building REAL300000300159 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300159' /scratch/stefan/7770550/working/building/REAL300000300159 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300159 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300159/0 /scratch/stefan/7770550/working/building/REAL300000300159 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/226 `/scratch/stefan/7770550/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C=C1F) `REAL300000300159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300159 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 15, 19, 19, 19, 19, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300159 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300159 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300159/1 /scratch/stefan/7770550/working/building/REAL300000300159 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/227 `/scratch/stefan/7770550/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1F) `REAL300000300159.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300159 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 14, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300159 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 11, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300159 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300159 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300159/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300159/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300159 Building REAL300000300160 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300160' /scratch/stefan/7770550/working/building/REAL300000300160 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300160 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300160/0 /scratch/stefan/7770550/working/building/REAL300000300160 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/228 `/scratch/stefan/7770550/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(F)=C1) `REAL300000300160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300160 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300160 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300160 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300160/1 /scratch/stefan/7770550/working/building/REAL300000300160 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/229 `/scratch/stefan/7770550/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(F)=C1) `REAL300000300160.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300160 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300160 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300160 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300160 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300160/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300160/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300160 Building REAL300000300161 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300161' /scratch/stefan/7770550/working/building/REAL300000300161 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300161 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300161/0 /scratch/stefan/7770550/working/building/REAL300000300161 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/230 `/scratch/stefan/7770550/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(F)=C1) `REAL300000300161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300161 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 7, 9, 9, 9, 9, 9, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 7, 1, 1, 1] 9 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300161 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300161 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300161/1 /scratch/stefan/7770550/working/building/REAL300000300161 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/231 `/scratch/stefan/7770550/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(F)=C1) `REAL300000300161.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300161 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 8, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1] 9 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300161 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300161 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300161 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300161/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300161/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300161 Building REAL300000300162 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300162' /scratch/stefan/7770550/working/building/REAL300000300162 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300162 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300162/0 /scratch/stefan/7770550/working/building/REAL300000300162 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/232 `/scratch/stefan/7770550/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C(C)=CC(C)=C1C) `REAL300000300162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300162 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C(C)=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 5, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 14, 19, 19, 19, 19, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 13, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2] 19 rigid atoms, others: [37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 118 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300162 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C(C)=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 5, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 16, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 16, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300162 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300162 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300162/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300162 Building REAL300000300163 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300163' /scratch/stefan/7770550/working/building/REAL300000300163 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300163 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300163/0 /scratch/stefan/7770550/working/building/REAL300000300163 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/233 `/scratch/stefan/7770550/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCOC2=C1) `REAL300000300163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300163 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 12, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300163 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300163 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300163 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300163/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300163 Building REAL300000300164 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300164' /scratch/stefan/7770550/working/building/REAL300000300164 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300164 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300164/0 /scratch/stefan/7770550/working/building/REAL300000300164 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/234 `/scratch/stefan/7770550/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1) `REAL300000300164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300164 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5] 5 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 21 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300164 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 9, 9, 5, 9, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 20, 21, 22, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 64 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300164 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300164 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300164/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300164 Building REAL300000300165 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300165' /scratch/stefan/7770550/working/building/REAL300000300165 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300165 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300165/0 /scratch/stefan/7770550/working/building/REAL300000300165 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/235 `/scratch/stefan/7770550/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300165 none CC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 36, 41, 41, 41, 41, 41, 41, 21, 8, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 8, 1, 1, 1, 2, 2, 2] 41 rigid atoms, others: [41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300165 none CC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5, 13, 41, 41, 15, 23, 41, 41, 41, 41, 41, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 13, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 9, 10, 11, 28, 29] set([6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300165 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300165 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300165/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300165 Building REAL300000300166 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300166' /scratch/stefan/7770550/working/building/REAL300000300166 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300166 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300166/0 /scratch/stefan/7770550/working/building/REAL300000300166 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/236 `/scratch/stefan/7770550/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1) `REAL300000300166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300166 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1] 9 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300166 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300166 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300166 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300166/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300166 Building REAL300000300167 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300167' /scratch/stefan/7770550/working/building/REAL300000300167 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300167 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300167/0 /scratch/stefan/7770550/working/building/REAL300000300167 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/237 `/scratch/stefan/7770550/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C=C1) `REAL300000300167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300167 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 7, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1] 9 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300167 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300167 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300167 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300167/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300167 Building REAL300000300168 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300168' /scratch/stefan/7770550/working/building/REAL300000300168 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300168 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300168/0 /scratch/stefan/7770550/working/building/REAL300000300168 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/238 `/scratch/stefan/7770550/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1) `REAL300000300168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300168 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1] 9 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300168 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300168 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300168/1 /scratch/stefan/7770550/working/building/REAL300000300168 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/239 `/scratch/stefan/7770550/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1) `REAL300000300168.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300168 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 9 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 25, 26, 27, 28]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300168 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300168 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300168 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300168/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300168/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300168 Building REAL300000300169 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300169' /scratch/stefan/7770550/working/building/REAL300000300169 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300169 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300169/0 /scratch/stefan/7770550/working/building/REAL300000300169 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/240 `/scratch/stefan/7770550/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300169 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 29, 29, 29, 29, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 29 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300169 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 13, 17, 17, 17, 17, 17, 17, 1, 1, 3, 3, 3, 3, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 29 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 38, 28, 29, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300169 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300169 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300169/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300169 Building REAL300000300170 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300170' /scratch/stefan/7770550/working/building/REAL300000300170 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300170 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300170/0 /scratch/stefan/7770550/working/building/REAL300000300170 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/241 `/scratch/stefan/7770550/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300170 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 12, 7, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 1, 1, 1, 2, 2, 2] 20 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300170 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300170 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300170 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300170/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300170 Building REAL300000300171 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300171' /scratch/stefan/7770550/working/building/REAL300000300171 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300171 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300171/0 /scratch/stefan/7770550/working/building/REAL300000300171 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/242 `/scratch/stefan/7770550/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(NC(=O)C(C)(C)C)C=C1) `REAL300000300171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300171 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(NC(=O)C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 41 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 46, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300171 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(NC(=O)C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 41, 41, 41, 41, 41, 41, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 9, 9] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300171 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300171 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300171/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300171 Building REAL300000300172 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300172' /scratch/stefan/7770550/working/building/REAL300000300172 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300172 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300172/0 /scratch/stefan/7770550/working/building/REAL300000300172 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/243 `/scratch/stefan/7770550/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C) `REAL300000300172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300172 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 15, 15, 15, 15, 15, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 1, 1, 2, 2, 2, 2, 2, 2] 15 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300172 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 59 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300172 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300172 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300172/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300172 Building REAL300000300173 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300173' /scratch/stefan/7770550/working/building/REAL300000300173 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300173 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300173/0 /scratch/stefan/7770550/working/building/REAL300000300173 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/244 `/scratch/stefan/7770550/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300173 none COC1=CC(Cl)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 41, 41, 41, 41, 41, 41, 41, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 45, 45, 45, 41, 41, 41, 1, 1, 1, 2, 2, 2] 45 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300173 none COC1=CC(Cl)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 41, 41, 25, 25, 41, 41, 41, 41, 41, 3, 3, 3, 1, 1, 1, 41, 41, 41, 41, 41, 41] 45 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300173 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300173/1 /scratch/stefan/7770550/working/building/REAL300000300173 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/245 `/scratch/stefan/7770550/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300173.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300173 none COC1=CC(Cl)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 21, 35, 35, 35, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 5, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300173 none COC1=CC(Cl)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 35, 35, 19, 31, 35, 35, 35, 35, 35, 3, 3, 3, 1, 1, 1, 19, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300173 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300173 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300173/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300173/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300173 Building REAL300000300174 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300174' /scratch/stefan/7770550/working/building/REAL300000300174 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300174 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300174/0 /scratch/stefan/7770550/working/building/REAL300000300174 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/246 `/scratch/stefan/7770550/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Br)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300174 none CC1=CC=C(Br)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 32, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300174 none CC1=CC=C(Br)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 19, 19, 15, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 11, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300174 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300174 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300174/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300174 Building REAL300000300175 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300175' /scratch/stefan/7770550/working/building/REAL300000300175 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300175 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300175/0 /scratch/stefan/7770550/working/building/REAL300000300175 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/247 `/scratch/stefan/7770550/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F) `REAL300000300175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300175 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 15, 21, 23, 23, 23, 23, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1] 23 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300175 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300175 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300175/1 /scratch/stefan/7770550/working/building/REAL300000300175 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/248 `/scratch/stefan/7770550/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F) `REAL300000300175.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300175 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 14, 23, 23, 23, 23, 23, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 13, 1, 1, 1] 23 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300175 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300175 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300175 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300175/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300175/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300175 Building REAL300000300176 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300176' /scratch/stefan/7770550/working/building/REAL300000300176 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300176 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300176/0 /scratch/stefan/7770550/working/building/REAL300000300176 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/249 `/scratch/stefan/7770550/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)SC(Cl)=C1) `REAL300000300176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300176 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)SC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 14, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 14, 14, 27, 27, 27, 27, 14, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300176 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)SC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 14, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300176 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300176 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300176/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300176 Building REAL300000300177 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300177' /scratch/stefan/7770550/working/building/REAL300000300177 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300177 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300177/0 /scratch/stefan/7770550/working/building/REAL300000300177 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/250 `/scratch/stefan/7770550/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCC(C)C)C=C1) `REAL300000300177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300177 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 11, 11, 11, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 63 rigid atoms, others: [32, 33, 11, 45, 14, 15, 16, 17, 18, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300177 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 49, 63, 63, 63, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 49, 49, 63, 63, 63, 63, 63, 63, 63, 63, 63, 9, 9] 63 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300177 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300177 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300177/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300177 Building REAL300000300178 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300178' /scratch/stefan/7770550/working/building/REAL300000300178 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300178 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300178/0 /scratch/stefan/7770550/working/building/REAL300000300178 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/251 `/scratch/stefan/7770550/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1C) `REAL300000300178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300178 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 19, 19, 19, 19, 19, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 13, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300178 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300178 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300178/1 /scratch/stefan/7770550/working/building/REAL300000300178 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/252 `/scratch/stefan/7770550/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1C) `REAL300000300178.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300178 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 17, 27, 27, 27, 27, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300178 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300178 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300178 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300178/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300178/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300178 Building REAL300000300179 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300179' /scratch/stefan/7770550/working/building/REAL300000300179 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300179 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300179/0 /scratch/stefan/7770550/working/building/REAL300000300179 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/253 `/scratch/stefan/7770550/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1F) `REAL300000300179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300179 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 13, 13, 27, 27, 27, 27, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300179 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300179 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300179 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300179/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300179 Building REAL300000300180 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300180' /scratch/stefan/7770550/working/building/REAL300000300180 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300180 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300180/0 /scratch/stefan/7770550/working/building/REAL300000300180 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/254 `/scratch/stefan/7770550/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1) `REAL300000300180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300180 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 5, 9, 11, 11, 11, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 11, 15, 15, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 7, 7, 11, 11, 1, 1] 53 rigid atoms, others: [32, 33, 38, 39, 11, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300180 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 35, 53, 53, 53, 11, 11, 2, 2, 2, 1, 1, 1, 5, 11, 11, 35, 35, 53, 53, 11, 11] 53 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300180 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300180 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300180/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300180 Building REAL300000300181 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300181' /scratch/stefan/7770550/working/building/REAL300000300181 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300181 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300181/0 /scratch/stefan/7770550/working/building/REAL300000300181 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/255 `/scratch/stefan/7770550/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300181 none CCC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 43, 43, 43, 19, 19, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 67, 67, 67, 67, 67, 43, 19, 19, 5, 1, 1, 1, 2, 2, 2, 19, 19] 67 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300181 none CCC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 12, 17, 19, 19, 19, 19, 19, 1, 1, 11, 11, 11, 11, 11, 5, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1] 67 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 40, 41, 23, 24, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300181 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300181 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300181/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300181 Building REAL300000300182 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300182' /scratch/stefan/7770550/working/building/REAL300000300182 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300182 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300182/0 /scratch/stefan/7770550/working/building/REAL300000300182 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/256 `/scratch/stefan/7770550/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)NC2=C1) `REAL300000300182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300182 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300182 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300182 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300182/1 /scratch/stefan/7770550/working/building/REAL300000300182 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/257 `/scratch/stefan/7770550/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)NC2=C1) `REAL300000300182.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300182 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300182 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300182 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300182 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300182/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300182/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300182 Building REAL300000300183 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300183' /scratch/stefan/7770550/working/building/REAL300000300183 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300183 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300183/0 /scratch/stefan/7770550/working/building/REAL300000300183 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/258 `/scratch/stefan/7770550/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(F)(F)F)C=C1) `REAL300000300183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300183 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 6, 9, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 15, 15, 1, 1] 63 rigid atoms, others: [33, 34, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 93 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300183 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 35, 63, 63, 63, 63, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 63, 63, 11, 11] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 221 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300183 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300183 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300183/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300183 Building REAL300000300184 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300184' /scratch/stefan/7770550/working/building/REAL300000300184 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300184 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300184/0 /scratch/stefan/7770550/working/building/REAL300000300184 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/259 `/scratch/stefan/7770550/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300184 none CSC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 21, 21, 21, 21, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 29, 29, 29, 21, 21, 5, 1, 1, 1, 2, 2, 2, 21, 21] 29 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300184 none CSC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 4, 4, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1, 1] 29 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 35, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300184 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300184 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300184/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300184 Building REAL300000300185 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300185' /scratch/stefan/7770550/working/building/REAL300000300185 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300185 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300185/0 /scratch/stefan/7770550/working/building/REAL300000300185 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/260 `/scratch/stefan/7770550/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CC2=C1) `REAL300000300185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300185 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300185 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300185 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300185 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300185/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300185 Building REAL300000300186 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300186' /scratch/stefan/7770550/working/building/REAL300000300186 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300186 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300186/0 /scratch/stefan/7770550/working/building/REAL300000300186 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/261 `/scratch/stefan/7770550/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CCC2=C1) `REAL300000300186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300186 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 14, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300186 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300186 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300186 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300186/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300186 Building REAL300000300187 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300187' /scratch/stefan/7770550/working/building/REAL300000300187 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300187 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300187/0 /scratch/stefan/7770550/working/building/REAL300000300187 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/262 `/scratch/stefan/7770550/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OCC) `REAL300000300187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300187 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OCC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [130, 72, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 80, 137, 130, 130, 130, 130, 130, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 137, 137, 137, 137, 137] 190 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 782 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300187 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OCC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [37, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 32, 37, 37, 37, 37, 37, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 32, 32, 32, 32, 32] 190 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 252 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300187 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300187 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300187/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300187 Building REAL300000300188 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300188' /scratch/stefan/7770550/working/building/REAL300000300188 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300188 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300188/0 /scratch/stefan/7770550/working/building/REAL300000300188 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/263 `/scratch/stefan/7770550/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2C=NN=N2)C=C1) `REAL300000300188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300188 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2C=NN=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 3, 1, 1] 17 rigid atoms, others: [32, 33, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300188 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2C=NN=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 17, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300188 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2C=NN=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 2, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 9, 3, 3, 1, 3, 3] 17 rigid atoms, others: [34, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300188 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300188 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300188/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300188 Building REAL300000300189 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300189' /scratch/stefan/7770550/working/building/REAL300000300189 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300189 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300189/0 /scratch/stefan/7770550/working/building/REAL300000300189 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/264 `/scratch/stefan/7770550/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CS1) `REAL300000300189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300189 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 18, 23, 23, 23, 23, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300189 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300189 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300189 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300189/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300189 Building REAL300000300190 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300190' /scratch/stefan/7770550/working/building/REAL300000300190 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300190 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300190/0 /scratch/stefan/7770550/working/building/REAL300000300190 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/265 `/scratch/stefan/7770550/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)OC2=C1) `REAL300000300190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300190 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300190 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300190 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300190/1 /scratch/stefan/7770550/working/building/REAL300000300190 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/266 `/scratch/stefan/7770550/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)OC2=C1) `REAL300000300190.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300190 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300190 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300190 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300190 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300190/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300190/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300190 Building REAL300000300191 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300191' /scratch/stefan/7770550/working/building/REAL300000300191 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300191 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300191/0 /scratch/stefan/7770550/working/building/REAL300000300191 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/267 `/scratch/stefan/7770550/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300191 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 2, 2, 2] 15 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300191 none CC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 15, 15, 12, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300191 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300191 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300191/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300191 Building REAL300000300192 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300192' /scratch/stefan/7770550/working/building/REAL300000300192 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300192 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300192/0 /scratch/stefan/7770550/working/building/REAL300000300192 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/268 `/scratch/stefan/7770550/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300192 none CC1=NN(C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 2, 2, 2] 28 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300192 none CC1=NN(C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 19, 28, 28, 19, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300192 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300192/1 /scratch/stefan/7770550/working/building/REAL300000300192 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/269 `/scratch/stefan/7770550/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300192.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300192 none CC1=NN(C)C(C)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300192 none CC1=NN(C)C(C)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 19, 27, 27, 25, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300192 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300192 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300192/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300192/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300192 Building REAL300000300193 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300193' /scratch/stefan/7770550/working/building/REAL300000300193 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300193 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300193/0 /scratch/stefan/7770550/working/building/REAL300000300193 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/270 `/scratch/stefan/7770550/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300193 none CNS(=O)(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 17, 27, 27, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 27, 27, 27, 27, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 27 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300193 none CNS(=O)(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 7, 7, 7, 7, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 27 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 39, 24, 29, 30, 31] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300193 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300193/1 /scratch/stefan/7770550/working/building/REAL300000300193 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/271 `/scratch/stefan/7770550/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300193.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300193/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300193 none CNS(=O)(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 21, 21, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 21, 21, 21, 21, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 21 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300193 none CNS(=O)(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 16, 17, 17, 17, 17, 17, 17, 1, 5, 5, 5, 5, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1] 21 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 24, 38, 29, 30, 31] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300193 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300193 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300193/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300193/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300193 Building REAL300000300194 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300194' /scratch/stefan/7770550/working/building/REAL300000300194 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300194 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300194/0 /scratch/stefan/7770550/working/building/REAL300000300194 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/272 `/scratch/stefan/7770550/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=CC(C)=C1C) `REAL300000300194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300194 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 12, 19, 19, 19, 19, 19, 11, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 2, 2, 2, 2, 2, 2] 19 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 90 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300194 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 19, 13, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 13, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 91 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300194 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300194/1 /scratch/stefan/7770550/working/building/REAL300000300194 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/273 `/scratch/stefan/7770550/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=CC(C)=C1C) `REAL300000300194.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300194 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 19, 19, 27, 27, 27, 27, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 2, 2, 2, 2, 2, 2] 27 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 114 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300194 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 76 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300194 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300194 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300194/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300194/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300194 Building REAL300000300195 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300195' /scratch/stefan/7770550/working/building/REAL300000300195 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300195 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300195/0 /scratch/stefan/7770550/working/building/REAL300000300195 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/274 `/scratch/stefan/7770550/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2CC1C) `REAL300000300195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300195 none CC(=O)N1C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 18, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 18, 18, 18, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17] 18 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300195 none CC(=O)N1C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 12, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2] 18 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 42, 39, 40, 22, 23, 24, 25, 26, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300195 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300195 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300195/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300195 Building REAL300000300196 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300196' /scratch/stefan/7770550/working/building/REAL300000300196 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300196 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300196/0 /scratch/stefan/7770550/working/building/REAL300000300196 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/275 `/scratch/stefan/7770550/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300196 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 17, 27, 9, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 27, 27, 27, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 27 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300196 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 27 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 36, 27, 28, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300196 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300196/1 /scratch/stefan/7770550/working/building/REAL300000300196 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/276 `/scratch/stefan/7770550/working/3D/276' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300196.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300196 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 17, 29, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 29, 29, 29, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17] 29 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300196 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1] 29 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 22, 23, 36, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300196 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300196 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300196/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300196/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300196 Building REAL300000300197 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300197' /scratch/stefan/7770550/working/building/REAL300000300197 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300197 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300197/0 /scratch/stefan/7770550/working/building/REAL300000300197 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/277 `/scratch/stefan/7770550/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300197 none CNC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 9, 17, 9, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 17 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300197 none CNC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 3, 3, 3, 3, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 38, 28, 29, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300197 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300197/1 /scratch/stefan/7770550/working/building/REAL300000300197 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/278 `/scratch/stefan/7770550/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300197.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300197 none CNC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19, 19] 19 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300197 none CNC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 1, 3, 3, 3, 3, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 36, 28, 29, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300197 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300197 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300197/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300197/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300197 Building REAL300000300198 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300198' /scratch/stefan/7770550/working/building/REAL300000300198 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300198 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300198/0 /scratch/stefan/7770550/working/building/REAL300000300198 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/279 `/scratch/stefan/7770550/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(N)(=O)=O)C=C1) `REAL300000300198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300198 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 5, 5, 1, 1] 33 rigid atoms, others: [32, 35, 36, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300198 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 33, 33, 33, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 33, 33, 9, 9] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300198 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300198/1 /scratch/stefan/7770550/working/building/REAL300000300198 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/280 `/scratch/stefan/7770550/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(N)(=O)=O)C=C1) `REAL300000300198.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300198 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 5, 5, 1, 1] 33 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 33, 19, 20, 21, 24, 25, 26, 27, 28, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300198 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(N)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 33, 33, 33, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 33, 33, 9, 9] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300198 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300198 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300198/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300198/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300198 Building REAL300000300199 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300199' /scratch/stefan/7770550/working/building/REAL300000300199 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300199 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300199/0 /scratch/stefan/7770550/working/building/REAL300000300199 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/281 `/scratch/stefan/7770550/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)F)C(Cl)=C1) `REAL300000300199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300199 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 9, 17, 19, 19, 19, 19, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 9, 20, 20, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 20, 1] 93 rigid atoms, others: [32, 33, 35, 11, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 157 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300199 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 19, 19, 19, 19, 69, 93, 93, 19, 19, 19, 2, 2, 2, 1, 1, 1, 5, 19, 19, 93, 19] 93 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 277 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300199 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300199 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300199/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300199 Building REAL300000300200 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300200' /scratch/stefan/7770550/working/building/REAL300000300200 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300200 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300200/0 /scratch/stefan/7770550/working/building/REAL300000300200 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/282 `/scratch/stefan/7770550/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2CCCC2=O)C=C1) `REAL300000300200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300200 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2CCCC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1] 33 rigid atoms, others: [33, 34, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300200 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2CCCC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 33, 33, 33, 33, 33, 33, 9, 9] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300200 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2CCCC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 17, 33, 33, 33, 33, 33, 17, 5, 4, 5, 5, 3, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 33, 33, 33, 33, 33, 33, 17, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5] 33 rigid atoms, others: [35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42]) total number of confs: 162 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300200 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300200 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300200/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300200 Building REAL300000300201 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300201' /scratch/stefan/7770550/working/building/REAL300000300201 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300201 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300201/0 /scratch/stefan/7770550/working/building/REAL300000300201 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/283 `/scratch/stefan/7770550/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=CC=C21) `REAL300000300201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300201 none CC(=O)N1CCCC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 17 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300201 none CC(=O)N1CCCC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 10, 7, 44, 45, 35, 25, 24, 36, 26, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300201 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300201 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300201/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300201 Building REAL300000300202 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300202' /scratch/stefan/7770550/working/building/REAL300000300202 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300202 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300202/0 /scratch/stefan/7770550/working/building/REAL300000300202 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/284 `/scratch/stefan/7770550/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300202 none COC(=O)C1=C(C)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 29, 47, 29, 29, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 47, 47, 47, 29, 29, 29, 29, 29, 29, 1, 1, 1, 2, 2, 2] 47 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300202 none COC(=O)C1=C(C)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 29, 29, 15, 24, 29, 29, 29, 29, 29, 5, 5, 5, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29, 29] 47 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300202 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300202/1 /scratch/stefan/7770550/working/building/REAL300000300202 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/285 `/scratch/stefan/7770550/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300202.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300202 none COC(=O)C1=C(C)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 35, 19, 19, 19, 13, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300202 none COC(=O)C1=C(C)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 9, 19, 19, 19, 19, 19, 19, 7, 7, 7, 2, 2, 2, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300202 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300202 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300202/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300202/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300202 Building REAL300000300203 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300203' /scratch/stefan/7770550/working/building/REAL300000300203 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300203 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300203/0 /scratch/stefan/7770550/working/building/REAL300000300203 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/286 `/scratch/stefan/7770550/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(N)=O)C=C1) `REAL300000300203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300203 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(N)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 2, 2, 1, 1] 17 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 19, 20, 32, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300203 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(N)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 17, 17, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300203 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300203/1 /scratch/stefan/7770550/working/building/REAL300000300203 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/287 `/scratch/stefan/7770550/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(N)=O)C=C1) `REAL300000300203.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300203 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(N)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 1, 1] 17 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 32, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300203 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(N)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 17, 17, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300203 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300203 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300203/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300203/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300203 Building REAL300000300204 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300204' /scratch/stefan/7770550/working/building/REAL300000300204 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300204 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300204/0 /scratch/stefan/7770550/working/building/REAL300000300204 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/288 `/scratch/stefan/7770550/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=CC=C21) `REAL300000300204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300204 none CC(=O)N1CCC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 17 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300204 none CC(=O)N1CCC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 9, 42, 7, 41, 23, 24, 25, 33, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300204 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300204 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300204/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300204 Building REAL300000300205 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300205' /scratch/stefan/7770550/working/building/REAL300000300205 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300205 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300205/0 /scratch/stefan/7770550/working/building/REAL300000300205 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/289 `/scratch/stefan/7770550/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300205 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 17 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300205 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 11, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 36, 27, 28, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300205 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300205 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300205/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300205 Building REAL300000300206 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300206' /scratch/stefan/7770550/working/building/REAL300000300206 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300206 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300206/0 /scratch/stefan/7770550/working/building/REAL300000300206 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/290 `/scratch/stefan/7770550/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2C=C1) `REAL300000300206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300206 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300206 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300206 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300206/1 /scratch/stefan/7770550/working/building/REAL300000300206 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/291 `/scratch/stefan/7770550/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2C=C1) `REAL300000300206.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300206 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300206 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300206 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300206 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300206/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300206/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300206 Building REAL300000300207 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300207' /scratch/stefan/7770550/working/building/REAL300000300207 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300207 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300207/0 /scratch/stefan/7770550/working/building/REAL300000300207 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/292 `/scratch/stefan/7770550/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=CS1) `REAL300000300207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300207 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=CS1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 28, 40, 28, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 40, 40, 40, 1, 1, 1, 2, 2, 2, 28, 28] 40 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 20, 21, 22, 23, 24, 25, 33, 29, 30, 31]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300207 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=CS1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 7, 7, 7, 17, 28, 28, 17, 25, 28, 28, 28, 28, 28, 1, 1, 1, 9, 9, 9, 28, 28, 28, 28, 28, 28, 1, 1] 40 rigid atoms, others: [32, 33, 2, 4, 5, 6, 20, 21, 22] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300207 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300207 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300207/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300207 Building REAL300000300208 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300208' /scratch/stefan/7770550/working/building/REAL300000300208 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300208 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300208/0 /scratch/stefan/7770550/working/building/REAL300000300208 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/293 `/scratch/stefan/7770550/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300208 none COCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 31, 19, 19, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 63, 63, 63, 63, 63, 31, 31, 19, 19, 5, 1, 1, 1, 2, 2, 2, 19, 19] 63 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300208 none COCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 6, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 1, 12, 12, 12, 6, 6, 4, 4, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1] 63 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 40, 22, 23, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300208 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300208 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300208/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300208 Building REAL300000300209 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300209' /scratch/stefan/7770550/working/building/REAL300000300209 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300209 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300209/0 /scratch/stefan/7770550/working/building/REAL300000300209 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/294 `/scratch/stefan/7770550/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1) `REAL300000300209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300209 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 8, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16] 16 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300209 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 16, 16, 7, 9, 16, 16, 16, 16, 16, 1, 1, 1, 3, 3, 3, 1, 2, 2, 2, 5, 16, 16, 16, 16, 16, 16, 2, 2, 2, 1] 16 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 41, 21, 22, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300209 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300209 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300209/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300209 Building REAL300000300210 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300210' /scratch/stefan/7770550/working/building/REAL300000300210 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300210 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300210/0 /scratch/stefan/7770550/working/building/REAL300000300210 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/295 `/scratch/stefan/7770550/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1) `REAL300000300210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300210 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 11, 7, 9, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 26, 37, 37, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 26, 26, 1, 1] 97 rigid atoms, others: [32, 33, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 161 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300210 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 47, 97, 97, 97, 11, 11, 2, 2, 2, 1, 1, 1, 5, 11, 11, 97, 97, 11, 11] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 345 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300210 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300210 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300210/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300210 Building REAL300000300211 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300211' /scratch/stefan/7770550/working/building/REAL300000300211 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300211 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300211/0 /scratch/stefan/7770550/working/building/REAL300000300211 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/296 `/scratch/stefan/7770550/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300211 none COCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 71, 17, 10, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 201, 201, 201, 201, 201, 143, 143, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 201 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 789 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300211 none COCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 47, 26, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 62, 62, 62, 47, 47, 26, 26, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 42, 23, 24, 25] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300211 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300211 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300211/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300211 Building REAL300000300212 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300212' /scratch/stefan/7770550/working/building/REAL300000300212 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300212 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300212/0 /scratch/stefan/7770550/working/building/REAL300000300212 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/297 `/scratch/stefan/7770550/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)CC1=CC=CC=C12) `REAL300000300212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300212 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 10, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300212 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)CC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300212 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300212 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300212/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300212 Building REAL300000300213 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300213' /scratch/stefan/7770550/working/building/REAL300000300213 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300213 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300213/0 /scratch/stefan/7770550/working/building/REAL300000300213 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/298 `/scratch/stefan/7770550/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC(C)C)C=C1) `REAL300000300213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300213 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 27 rigid atoms, others: [32, 43, 42, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300213 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300213 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300213 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300213/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300213 Building REAL300000300214 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300214' /scratch/stefan/7770550/working/building/REAL300000300214 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300214 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300214/0 /scratch/stefan/7770550/working/building/REAL300000300214 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/299 `/scratch/stefan/7770550/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1) `REAL300000300214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300214 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 7, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1] 9 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300214 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300214 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300214 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300214/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300214 Building REAL300000300215 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300215' /scratch/stefan/7770550/working/building/REAL300000300215 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300215 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300215/0 /scratch/stefan/7770550/working/building/REAL300000300215 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/300 `/scratch/stefan/7770550/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1F) `REAL300000300215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300215 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 14, 14, 19, 19, 19, 19, 14, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300215 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300215 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300215/1 /scratch/stefan/7770550/working/building/REAL300000300215 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/301 `/scratch/stefan/7770550/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1F) `REAL300000300215.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300215 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300215 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300215 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300215 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300215/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300215/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300215 Building REAL300000300216 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300216' /scratch/stefan/7770550/working/building/REAL300000300216 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300000300216 as failed and skipping /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `/scratch/stefan/7770550/failed' `/scratch/stefan/7770550/working/building/REAL300000300216' -> `/scratch/stefan/7770550/failed/REAL300000300216' Building REAL300000300217 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300217' /scratch/stefan/7770550/working/building/REAL300000300217 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300217 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300217/0 /scratch/stefan/7770550/working/building/REAL300000300217 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/302 `/scratch/stefan/7770550/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)C2) `REAL300000300217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300217 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 13, 17, 17, 17, 17, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300217 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300217 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300217/1 /scratch/stefan/7770550/working/building/REAL300000300217 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/303 `/scratch/stefan/7770550/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)C2) `REAL300000300217.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300217 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300217 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300217 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300217 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300217/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300217/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300217 Building REAL300000300218 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300218' /scratch/stefan/7770550/working/building/REAL300000300218 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300218 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300218/0 /scratch/stefan/7770550/working/building/REAL300000300218 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/304 `/scratch/stefan/7770550/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C2=NC=CC=C12) `REAL300000300218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300218 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 11, 15, 15, 15, 15, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 1, 1, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300218 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300218 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300218/1 /scratch/stefan/7770550/working/building/REAL300000300218 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/305 `/scratch/stefan/7770550/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C2=NC=CC=C12) `REAL300000300218.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300218 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 13, 13, 13, 13, 13, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300218 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.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, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300218 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300218 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300218/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300218/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300218 Building REAL300000300219 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300219' /scratch/stefan/7770550/working/building/REAL300000300219 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300219 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300219/0 /scratch/stefan/7770550/working/building/REAL300000300219 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/306 `/scratch/stefan/7770550/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300219 none CCOC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 194, 82, 194, 82, 82, 82, 82, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 82, 82, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 522 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300219 none CCOC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 20, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 32, 82, 82, 32, 32, 82, 82, 82, 82, 82, 38, 38, 38, 38, 38, 1, 1, 82, 82, 82, 82, 82, 82] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 502 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300219 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300219 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300219/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300219 Building REAL300000300220 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300220' /scratch/stefan/7770550/working/building/REAL300000300220 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300220 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300220/0 /scratch/stefan/7770550/working/building/REAL300000300220 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/307 `/scratch/stefan/7770550/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)=C2N=C1) `REAL300000300220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300220 none CC1=CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2, 27] 27 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300220 none CC1=CC2=CC=CC(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 27, 27, 23, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 38, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300220 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300220/1 /scratch/stefan/7770550/working/building/REAL300000300220 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/308 `/scratch/stefan/7770550/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=C2N=C1) `REAL300000300220.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300220 none CC1=CC2=CC=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 1, 1, 1, 2, 2, 2, 25] 25 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300220 none CC1=CC2=CC=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 25, 25, 15, 22, 25, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 15, 25, 25, 25, 25, 25, 25, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 22, 23, 24, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300220 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300220 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300220/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300220/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300220 Building REAL300000300221 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300221' /scratch/stefan/7770550/working/building/REAL300000300221 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300221 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300221/0 /scratch/stefan/7770550/working/building/REAL300000300221 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/309 `/scratch/stefan/7770550/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300221 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 43, 23, 13, 23, 23, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 23, 23, 87, 87, 87, 87, 87, 87, 87, 23, 23, 7, 1, 1, 1, 2, 2, 2, 23, 23] 87 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 369 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300221 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 10, 17, 23, 23, 23, 23, 23, 1, 1, 17, 18, 18, 17, 17, 13, 13, 1, 1, 9, 23, 23, 23, 23, 23, 23, 1, 1] 87 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 40, 22, 23, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 203 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300221 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300221 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300221/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300221 Building REAL300000300222 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300222' /scratch/stefan/7770550/working/building/REAL300000300222 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300222 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300222/0 /scratch/stefan/7770550/working/building/REAL300000300222 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/310 `/scratch/stefan/7770550/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1) `REAL300000300222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300222 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1, 2, 2, 2, 13] 13 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300222 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 13, 13, 7, 13, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 2, 1, 1, 7, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300222 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300222/1 /scratch/stefan/7770550/working/building/REAL300000300222 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/311 `/scratch/stefan/7770550/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1) `REAL300000300222.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300222 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 2, 13] 13 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300222 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 13, 13, 7, 7, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300222 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300222 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300222/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300222/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300222 Building REAL300000300223 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300223' /scratch/stefan/7770550/working/building/REAL300000300223 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300223 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300223/0 /scratch/stefan/7770550/working/building/REAL300000300223 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/312 `/scratch/stefan/7770550/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1OC(F)(F)F) `REAL300000300223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300223 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 25, 32, 59, 59, 59, 59, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 16, 15, 16, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1] 106 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300223 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 59, 59, 27, 59, 59, 59, 106, 106, 106, 106, 2, 2, 2, 1, 1, 1, 59, 59, 59, 59] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300223 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300223/1 /scratch/stefan/7770550/working/building/REAL300000300223 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/313 `/scratch/stefan/7770550/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1OC(F)(F)F) `REAL300000300223.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300223 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 24, 43, 58, 58, 58, 58, 24, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 8, 16, 16, 16, 58, 58, 58, 58, 58, 58, 24, 1, 1, 1, 1] 98 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300223 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 17, 17, 17, 58, 58, 27, 58, 58, 58, 98, 98, 98, 98, 2, 2, 2, 1, 1, 1, 7, 58, 58, 58, 58] 98 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300223 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300223 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300223/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300223/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300223 Building REAL300000300224 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300224' /scratch/stefan/7770550/working/building/REAL300000300224 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300224 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300224/0 /scratch/stefan/7770550/working/building/REAL300000300224 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/314 `/scratch/stefan/7770550/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCC(=O)NC2=C1) `REAL300000300224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300224 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300224 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300224 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300224 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300224/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300224 Building REAL300000300225 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300225' /scratch/stefan/7770550/working/building/REAL300000300225 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300225 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300225/0 /scratch/stefan/7770550/working/building/REAL300000300225 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/315 `/scratch/stefan/7770550/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(N)(=O)=O)=C1) `REAL300000300225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300225 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(N)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 12, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 5, 5, 1] 55 rigid atoms, others: [32, 33, 36, 11, 14, 15, 16, 17, 18, 19, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300225 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(N)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 55, 55, 55, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 55, 55, 17] 55 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300225 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300225/1 /scratch/stefan/7770550/working/building/REAL300000300225 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/316 `/scratch/stefan/7770550/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(N)(=O)=O)=C1) `REAL300000300225.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300225 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(N)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 1] 47 rigid atoms, others: [32, 35, 11, 14, 15, 16, 17, 18, 19, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300225 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(N)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 47, 47, 47, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 47, 47, 17] 47 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300225 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300225 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300225/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300225/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300225 Building REAL300000300226 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300226' /scratch/stefan/7770550/working/building/REAL300000300226 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300226 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300226/0 /scratch/stefan/7770550/working/building/REAL300000300226 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/317 `/scratch/stefan/7770550/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)CC(=O)N2C) `REAL300000300226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300226 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)CC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300226 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)CC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300226 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300226 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300226/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300226 Building REAL300000300227 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300227' /scratch/stefan/7770550/working/building/REAL300000300227 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300227 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300227/0 /scratch/stefan/7770550/working/building/REAL300000300227 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/318 `/scratch/stefan/7770550/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C([N+](=O)[O-])=C1) `REAL300000300227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300227 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300227 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 5, 5, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1, 3, 3, 3, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 24, 36, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300227 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300227 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300227/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300227 Building REAL300000300228 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300228' /scratch/stefan/7770550/working/building/REAL300000300228 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300228 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300228/0 /scratch/stefan/7770550/working/building/REAL300000300228 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/319 `/scratch/stefan/7770550/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=O)N(C)C(=O)C2=C1) `REAL300000300228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300228 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=O)N(C)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 2, 2, 2, 1] 17 rigid atoms, others: [33, 34, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300228 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=O)N(C)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300228 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300228/1 /scratch/stefan/7770550/working/building/REAL300000300228 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/320 `/scratch/stefan/7770550/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=O)N(C)C(=O)C2=C1) `REAL300000300228.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300228 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=O)N(C)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1] 17 rigid atoms, others: [32, 33, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300228 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=O)N(C)C(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300228 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300228 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300228/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300228/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300228 Building REAL300000300229 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300229' /scratch/stefan/7770550/working/building/REAL300000300229 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300229 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300229/0 /scratch/stefan/7770550/working/building/REAL300000300229 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/321 `/scratch/stefan/7770550/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(=O)C=CC2=C1) `REAL300000300229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300229 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(=O)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300229 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(=O)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300229 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300229 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300229/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300229 Building REAL300000300230 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300230' /scratch/stefan/7770550/working/building/REAL300000300230 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300230 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300230/0 /scratch/stefan/7770550/working/building/REAL300000300230 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/322 `/scratch/stefan/7770550/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)OC(=O)N2C) `REAL300000300230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300230 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)OC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300230 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)OC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300230 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300230/1 /scratch/stefan/7770550/working/building/REAL300000300230 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/323 `/scratch/stefan/7770550/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)OC(=O)N2C) `REAL300000300230.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300230 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)OC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300230 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)OC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300230 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300230 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300230/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300230/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300230 Building REAL300000300231 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300231' /scratch/stefan/7770550/working/building/REAL300000300231 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300231 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300231/0 /scratch/stefan/7770550/working/building/REAL300000300231 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/324 `/scratch/stefan/7770550/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(OC(F)(F)F)=C1) `REAL300000300231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300231 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(OC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 9, 17, 28, 28, 28, 28, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 12, 14, 14, 14, 1, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 1] 106 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300231 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(OC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 28, 28, 28, 28, 28, 106, 106, 106, 106, 28, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 28] 106 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300231 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300231/1 /scratch/stefan/7770550/working/building/REAL300000300231 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/325 `/scratch/stefan/7770550/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(OC(F)(F)F)=C1) `REAL300000300231.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300231 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(OC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 9, 17, 29, 29, 29, 29, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1] 114 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300231 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(OC(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 114, 114, 114, 114, 29, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29] 114 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300231 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300231 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300231/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300231/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300231 Building REAL300000300232 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300232' /scratch/stefan/7770550/working/building/REAL300000300232 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300232 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300232/0 /scratch/stefan/7770550/working/building/REAL300000300232 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/326 `/scratch/stefan/7770550/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(C)(=O)=O)C=C1) `REAL300000300232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300232 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 3, 3, 3, 1, 1] 17 rigid atoms, others: [32, 36, 37, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300232 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 17, 17, 17, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300232 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300232/1 /scratch/stefan/7770550/working/building/REAL300000300232 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/327 `/scratch/stefan/7770550/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(C)(=O)=O)C=C1) `REAL300000300232.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300232 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 3, 3, 3, 1, 1] 17 rigid atoms, others: [35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300232 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 17, 17, 17, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300232 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300232 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300232/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300232/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300232 Building REAL300000300233 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300233' /scratch/stefan/7770550/working/building/REAL300000300233 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300233 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300233/0 /scratch/stefan/7770550/working/building/REAL300000300233 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/328 `/scratch/stefan/7770550/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1C) `REAL300000300233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300233 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300233 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300233 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300233 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300233/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300233 Building REAL300000300234 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300234' /scratch/stefan/7770550/working/building/REAL300000300234 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300234 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300234/0 /scratch/stefan/7770550/working/building/REAL300000300234 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/329 `/scratch/stefan/7770550/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300234 none CNS(=O)(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 7, 1, 1, 1, 2, 2, 2, 23, 23] 23 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300234 none CNS(=O)(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 9, 17, 23, 23, 23, 23, 23, 1, 1, 3, 3, 3, 3, 1, 1, 9, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 23, 24, 38, 29, 30] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300234 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300234/1 /scratch/stefan/7770550/working/building/REAL300000300234 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/330 `/scratch/stefan/7770550/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300234.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300234 none CNS(=O)(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 14, 22, 22, 22, 22, 22, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 2, 2, 2, 22, 22] 22 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300234 none CNS(=O)(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 9, 17, 22, 22, 22, 22, 22, 1, 1, 3, 3, 3, 3, 1, 1, 22, 22, 22, 22, 22, 22, 1, 1] 22 rigid atoms, others: [2, 5, 6, 7, 8, 9, 23, 24, 38, 29, 30, 37] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300234 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300234 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300234/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300234/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300234 Building REAL300000300235 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300235' /scratch/stefan/7770550/working/building/REAL300000300235 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300235 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300235/0 /scratch/stefan/7770550/working/building/REAL300000300235 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/331 `/scratch/stefan/7770550/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C1=CC=CC=C1) `REAL300000300235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300235 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 14, 24, 24, 24, 24, 24, 14, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 24, 24, 24, 24, 24, 24, 14, 1, 1, 1, 1, 2, 2, 2, 2, 2] 24 rigid atoms, others: [33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300235 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300235 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 14, 24, 24, 24, 24, 24, 14, 7, 2, 7, 7, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 14, 2, 2, 2, 2, 1, 1, 1, 1, 1] 24 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300235 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300235/1 /scratch/stefan/7770550/working/building/REAL300000300235 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/332 `/scratch/stefan/7770550/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C1=CC=CC=C1) `REAL300000300235.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300235 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 13, 23, 25, 25, 25, 25, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 2, 2, 1, 2, 2] 25 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300235 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300235 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 13, 22, 25, 25, 25, 25, 13, 7, 2, 7, 7, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 2, 1, 2, 2, 1, 1, 1, 1, 1] 25 rigid atoms, others: [36, 37, 38, 39, 40, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300235 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300235 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300235/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300235/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300235 Building REAL300000300236 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300236' /scratch/stefan/7770550/working/building/REAL300000300236 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300236 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300236/0 /scratch/stefan/7770550/working/building/REAL300000300236 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/333 `/scratch/stefan/7770550/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1Cl) `REAL300000300236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300236 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 13, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300236 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300236 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300236/1 /scratch/stefan/7770550/working/building/REAL300000300236 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/334 `/scratch/stefan/7770550/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C=C1Cl) `REAL300000300236.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300236 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 7, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300236 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300236 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300236 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300236/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300236/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300236 Building REAL300000300237 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300237' /scratch/stefan/7770550/working/building/REAL300000300237 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300237 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300237/0 /scratch/stefan/7770550/working/building/REAL300000300237 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/335 `/scratch/stefan/7770550/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC(C(=O)N2CCCC2)=C1) `REAL300000300237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300237 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC(C(=O)N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 10, 10, 12, 12, 12, 12, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 1] 71 rigid atoms, others: [33, 34, 43, 11, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300237 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC(C(=O)N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 71, 71, 71, 71, 71, 71, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 71, 71, 71, 71, 71, 71, 71, 71, 17] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 197 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: REAL300000300237 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC(C(=O)N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 40, 42, 71, 71, 71, 71, 40, 18, 12, 18, 18, 12, 12, 12, 5, 1, 5, 1, 1, 1, 1, 1, 12, 71, 71, 71, 71, 71, 71, 40, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12] 71 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43]) total number of confs: 402 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300237 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300237/1 /scratch/stefan/7770550/working/building/REAL300000300237 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/336 `/scratch/stefan/7770550/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC(C(=O)N2CCCC2)=C1) `REAL300000300237.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300237 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC(C(=O)N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 1, 17, 17, 17, 17, 17, 17, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1] 44 rigid atoms, others: [32, 33, 42, 11, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300237 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC(C(=O)N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 44, 44, 44, 44, 44, 44, 17, 2, 2, 2, 1, 1, 1, 17, 17, 44, 44, 44, 44, 44, 44, 44, 44, 17] 44 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 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: REAL300000300237 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC(C(=O)N2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 44, 28, 14, 8, 14, 14, 8, 8, 8, 5, 1, 5, 1, 1, 1, 1, 1, 8, 44, 44, 44, 44, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8] 44 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 18, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42]) total number of confs: 106 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300237 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300237 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300237/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300237/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300237 Building REAL300000300238 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300238' /scratch/stefan/7770550/working/building/REAL300000300238 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300238 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300238/0 /scratch/stefan/7770550/working/building/REAL300000300238 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/337 `/scratch/stefan/7770550/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1) `REAL300000300238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300238 none CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 37, 37, 37, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 37, 37, 37, 49, 49, 49, 49, 37, 37, 1, 1, 1, 2, 2, 2, 37] 49 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300238 none CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 37, 37, 21, 33, 37, 37, 37, 37, 37, 1, 1, 1, 5, 5, 5, 5, 1, 1, 37, 37, 37, 37, 37, 37, 1] 49 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 24, 29, 30, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300238 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300238/1 /scratch/stefan/7770550/working/building/REAL300000300238 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/338 `/scratch/stefan/7770550/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1) `REAL300000300238.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300238 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 21, 17, 31, 31, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 56, 56, 56, 56, 31, 31, 5, 1, 1, 1, 2, 2, 2, 31] 56 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300238 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 6, 7, 7, 6, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 31, 31, 17, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 1, 1, 17, 31, 31, 31, 31, 31, 31, 1] 55 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 24, 38, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300238 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300238 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300238/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300238/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300238 Building REAL300000300239 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300239' /scratch/stefan/7770550/working/building/REAL300000300239 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300239 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300239/0 /scratch/stefan/7770550/working/building/REAL300000300239 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/339 `/scratch/stefan/7770550/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(C)(=O)=O)=C1) `REAL300000300239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300239 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 3, 3, 3, 1] 27 rigid atoms, others: [32, 33, 37, 11, 14, 15, 16, 17, 18, 19, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300239 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 27, 27, 27, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 27, 27, 27, 17] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300239 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300239/1 /scratch/stefan/7770550/working/building/REAL300000300239 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/340 `/scratch/stefan/7770550/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(C)(=O)=O)=C1) `REAL300000300239.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300239 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 3, 1] 25 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 19, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300239 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 25, 25, 25, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 25, 25, 25, 17] 25 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300239 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300239 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300239/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300239/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300239 Building REAL300000300240 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300240' /scratch/stefan/7770550/working/building/REAL300000300240 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300240 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300240/0 /scratch/stefan/7770550/working/building/REAL300000300240 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/341 `/scratch/stefan/7770550/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1)OC1=C2C=CC=C1) `REAL300000300240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300240 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1)OC1=C2C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 10, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300240 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1)OC1=C2C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300240 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300240/1 /scratch/stefan/7770550/working/building/REAL300000300240 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/342 `/scratch/stefan/7770550/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1)OC1=C2C=CC=C1) `REAL300000300240.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300240 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1)OC1=C2C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 27, 28, 29, 30, 31]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300240 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1)OC1=C2C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300240 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300240 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300240/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300240/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300240 Building REAL300000300241 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300241' /scratch/stefan/7770550/working/building/REAL300000300241 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300241 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300241/0 /scratch/stefan/7770550/working/building/REAL300000300241 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/343 `/scratch/stefan/7770550/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(=O)(=O)N(C)C)=C1) `REAL300000300241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300241 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(=O)(=O)N(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 16, 16, 16, 16, 16, 16, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1] 33 rigid atoms, others: [33, 34, 35, 42, 11, 14, 15, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300241 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(=O)(=O)N(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 16, 16, 9, 16, 16, 33, 33, 33, 33, 33, 16, 2, 2, 2, 1, 1, 1, 5, 16, 16, 9, 33, 33, 33, 33, 33, 33, 16] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300241 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300241/1 /scratch/stefan/7770550/working/building/REAL300000300241 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/344 `/scratch/stefan/7770550/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(=O)(=O)N(C)C)=C1) `REAL300000300241.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300241 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(=O)(=O)N(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 13, 13, 13, 13, 13, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1] 25 rigid atoms, others: [32, 33, 34, 41, 11, 14, 15, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300241 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(=O)(=O)N(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 13, 13, 9, 13, 13, 25, 25, 25, 25, 25, 13, 2, 2, 2, 1, 1, 1, 13, 13, 9, 25, 25, 25, 25, 25, 25, 13] 25 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300241 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300241 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300241/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300241/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300241 Building REAL300000300242 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300242' /scratch/stefan/7770550/working/building/REAL300000300242 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300242 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300242/0 /scratch/stefan/7770550/working/building/REAL300000300242 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/345 `/scratch/stefan/7770550/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCC2=CC=CC=C2C1) `REAL300000300242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300242 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 19, 19, 29, 29, 29, 29, 19, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 147 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300242 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300242 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300242 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300242/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300242 Building REAL300000300243 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300243' /scratch/stefan/7770550/working/building/REAL300000300243 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300243 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300243/0 /scratch/stefan/7770550/working/building/REAL300000300243 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/346 `/scratch/stefan/7770550/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1OC) `REAL300000300243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300243 none COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 43, 43, 43, 43, 43, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 43, 43, 43, 61, 61, 61, 61, 43, 1, 1, 1, 2, 2, 2, 43, 61, 61, 61] 61 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300243 none COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 43, 43, 22, 22, 43, 43, 43, 43, 43, 1, 1, 1, 4, 4, 4, 4, 1, 43, 43, 43, 43, 43, 43, 1, 4, 4, 4] 61 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300243 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300243/1 /scratch/stefan/7770550/working/building/REAL300000300243 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/347 `/scratch/stefan/7770550/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC) `REAL300000300243.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300243 none COC1=CC(F)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 42, 42, 42, 42, 42, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 67, 67, 67, 67, 42, 7, 1, 1, 1, 2, 2, 2, 42, 67, 67, 67] 67 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300243 none COC1=CC(F)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 42, 42, 22, 36, 42, 42, 42, 42, 42, 1, 1, 1, 4, 4, 4, 4, 1, 22, 42, 42, 42, 42, 42, 42, 1, 4, 4, 4] 67 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300243 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300243 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300243/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300243/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300243 Building REAL300000300244 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300244' /scratch/stefan/7770550/working/building/REAL300000300244 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300244 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300244/0 /scratch/stefan/7770550/working/building/REAL300000300244 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/348 `/scratch/stefan/7770550/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC) `REAL300000300244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300244 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 19, 19, 19, 19, 19, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 32, 32, 32, 32, 19, 19, 19, 19, 8, 1, 1, 1, 2, 2, 2, 19, 32, 32, 32] 32 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 123 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300244 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 19, 19, 5, 9, 19, 19, 19, 19, 19, 1, 1, 1, 4, 3, 3, 3, 1, 2, 2, 2, 5, 19, 19, 19, 19, 19, 19, 1, 4, 4, 4] 32 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300244 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300244 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300244/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300244 Building REAL300000300245 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300245' /scratch/stefan/7770550/working/building/REAL300000300245 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300245 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300245/0 /scratch/stefan/7770550/working/building/REAL300000300245 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/349 `/scratch/stefan/7770550/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1) `REAL300000300245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300245 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 7, 15, 15, 15, 15, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 2, 2, 2, 1] 15 rigid atoms, others: [34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300245 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300245 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300245/1 /scratch/stefan/7770550/working/building/REAL300000300245 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/350 `/scratch/stefan/7770550/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1) `REAL300000300245.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300245 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 7, 15, 15, 15, 15, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 1] 15 rigid atoms, others: [33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300245 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300245 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300245 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300245/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300245/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300245 Building REAL300000300246 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300246' /scratch/stefan/7770550/working/building/REAL300000300246 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300246 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300246/0 /scratch/stefan/7770550/working/building/REAL300000300246 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/351 `/scratch/stefan/7770550/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)N(C)C=N1) `REAL300000300246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300246 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 35, 55, 55, 55, 55, 35, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 2, 2, 2, 1] 55 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300246 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)N(C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 55, 55, 55, 55, 55, 55, 2, 2, 2, 1, 1, 1, 55, 55, 55, 55] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300246 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300246 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300246/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300246 Building REAL300000300247 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300247' /scratch/stefan/7770550/working/building/REAL300000300247 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300247 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300247/0 /scratch/stefan/7770550/working/building/REAL300000300247 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/352 `/scratch/stefan/7770550/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(Br)=C1) `REAL300000300247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300247 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 7, 1, 1, 1, 2, 2, 2, 11] 11 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300247 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 17, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 11, 11, 5, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 1, 5, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300247 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300247/1 /scratch/stefan/7770550/working/building/REAL300000300247 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/353 `/scratch/stefan/7770550/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(Br)=C1) `REAL300000300247.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300247 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 11] 11 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300247 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 11, 11, 5, 9, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300247 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300247 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300247/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300247/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300247 Building REAL300000300248 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300248' /scratch/stefan/7770550/working/building/REAL300000300248 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300248 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300248/0 /scratch/stefan/7770550/working/building/REAL300000300248 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/354 `/scratch/stefan/7770550/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN(C)C(C(N)=O)=C1) `REAL300000300248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300248 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN(C)C(C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 2, 2, 2, 2, 2, 1] 17 rigid atoms, others: [36, 11, 14, 15, 16, 17, 18, 19, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300248 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN(C)C(C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300248 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300248/1 /scratch/stefan/7770550/working/building/REAL300000300248 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/355 `/scratch/stefan/7770550/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)C(C(N)=O)=C1) `REAL300000300248.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300248 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)C(C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 2, 2, 1] 17 rigid atoms, others: [35, 11, 14, 15, 16, 17, 18, 19, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300248 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)C(C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300248 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300248 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300248/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300248/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300248 Building REAL300000300249 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300249' /scratch/stefan/7770550/working/building/REAL300000300249 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300249 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300249/0 /scratch/stefan/7770550/working/building/REAL300000300249 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/356 `/scratch/stefan/7770550/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C) `REAL300000300249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300249 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 15, 17, 17, 17, 17, 9, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 2, 1, 2, 2, 2] 34 rigid atoms, others: [32, 34, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 33, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300249 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(O)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 6, 17, 34, 17, 17, 17, 17] 34 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300249 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300249 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300249/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300249 Building REAL300000300250 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300250' /scratch/stefan/7770550/working/building/REAL300000300250 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300250 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300250/0 /scratch/stefan/7770550/working/building/REAL300000300250 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/357 `/scratch/stefan/7770550/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300250 none COC(=O)C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 21, 35, 21, 21, 21, 21, 21, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 35, 35, 35, 21, 21, 1, 1, 1, 2, 2, 2, 21] 35 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300250 none COC(=O)C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 9, 11, 21, 21, 21, 21, 21, 1, 10, 10, 10, 1, 1, 21, 21, 21, 21, 21, 21, 1] 35 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 36, 28, 29] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300250 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300250/1 /scratch/stefan/7770550/working/building/REAL300000300250 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/358 `/scratch/stefan/7770550/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300250.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300250 none COC(=O)C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 17, 41, 17, 17, 17, 17, 17, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 41, 41, 41, 17, 17, 7, 1, 1, 1, 2, 2, 2, 17] 41 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300250 none COC(=O)C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 17, 17, 9, 13, 17, 17, 17, 17, 17, 1, 11, 11, 11, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 41 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 28, 29, 37] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300250 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300250 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300250/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300250/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300250 Building REAL300000300251 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300251' /scratch/stefan/7770550/working/building/REAL300000300251 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300251 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300251/0 /scratch/stefan/7770550/working/building/REAL300000300251 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/359 `/scratch/stefan/7770550/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300251 none COCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 109, 53, 25, 15, 25, 25, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 25, 195, 195, 195, 195, 195, 109, 109, 25, 25, 7, 1, 1, 1, 2, 2, 2, 25, 25] 195 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 863 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300251 none COCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [52, 26, 11, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 10, 17, 25, 25, 25, 25, 25, 1, 1, 52, 52, 52, 26, 26, 11, 11, 1, 1, 9, 25, 25, 25, 25, 25, 25, 1, 1] 195 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 42, 41, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 272 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300251 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300251 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300251/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300251 Building REAL300000300252 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300252' /scratch/stefan/7770550/working/building/REAL300000300252 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300252 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300252/0 /scratch/stefan/7770550/working/building/REAL300000300252 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/360 `/scratch/stefan/7770550/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300252 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300252 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 1, 4, 4, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300252 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300252 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300252/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300252 Building REAL300000300253 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300253' /scratch/stefan/7770550/working/building/REAL300000300253 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300253 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300253/0 /scratch/stefan/7770550/working/building/REAL300000300253 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/361 `/scratch/stefan/7770550/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300253 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 7, 1, 1, 1, 2, 2, 2, 22] 22 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300253 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 9, 17, 22, 22, 22, 22, 22, 1, 1, 1, 4, 4, 4, 1, 1, 9, 22, 22, 22, 22, 22, 22, 1] 22 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300253 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300253 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300253/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300253 Building REAL300000300254 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300254' /scratch/stefan/7770550/working/building/REAL300000300254 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300254 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300254/0 /scratch/stefan/7770550/working/building/REAL300000300254 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/362 `/scratch/stefan/7770550/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300254 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 15, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 7, 1, 1, 1, 2, 2, 2, 27, 27, 27, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300254 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 27, 27, 9, 17, 27, 27, 27, 27, 27, 1, 1, 1, 4, 4, 4, 1, 1, 9, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300254 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300254 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300254/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300254 Building REAL300000300255 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300255' /scratch/stefan/7770550/working/building/REAL300000300255 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300255 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300255/0 /scratch/stefan/7770550/working/building/REAL300000300255 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/363 `/scratch/stefan/7770550/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300255 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 21, 11, 21, 21, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 43, 43, 43, 43, 43, 21, 21, 5, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21] 43 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 155 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300255 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 10, 17, 21, 21, 21, 21, 21, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2] 43 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 22, 23, 38, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300255 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300255 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300255/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300255 Building REAL300000300256 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300256' /scratch/stefan/7770550/working/building/REAL300000300256 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300256 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300256/0 /scratch/stefan/7770550/working/building/REAL300000300256 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/364 `/scratch/stefan/7770550/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(N)=O) `REAL300000300256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300256 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 33, 33] 33 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300256 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 3, 3] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 36, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300256 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300256 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300256/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300256 Building REAL300000300257 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300257' /scratch/stefan/7770550/working/building/REAL300000300257 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300257 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300257/0 /scratch/stefan/7770550/working/building/REAL300000300257 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/365 `/scratch/stefan/7770550/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(N)=O) `REAL300000300257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300257 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [44, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 47, 47, 44, 44, 44, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 47, 47] 47 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300257 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 15, 17, 17, 17, 17, 17, 17, 1, 1, 1, 4, 4, 3, 3, 3, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 4, 4] 47 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 38, 39]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300257 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300257 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300257/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300257 Building REAL300000300258 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300258' /scratch/stefan/7770550/working/building/REAL300000300258 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300258 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300258/0 /scratch/stefan/7770550/working/building/REAL300000300258 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/366 `/scratch/stefan/7770550/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)C2=CC=CC=C21) `REAL300000300258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300258 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 5, 5, 15, 15, 15, 15, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 6, 11, 11, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 35 rigid atoms, others: [35, 36, 47, 11, 44, 45, 14, 15, 16, 17, 18, 46, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300258 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 33, 35, 35, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 35, 35, 35, 35, 35, 35, 35, 15, 15, 15, 15] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300258 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300258/1 /scratch/stefan/7770550/working/building/REAL300000300258 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/367 `/scratch/stefan/7770550/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OC(C)C)C2=CC=CC=C21) `REAL300000300258.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300258 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OC(C)C)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 7, 11, 19, 19, 19, 19, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 6, 11, 11, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1] 41 rigid atoms, others: [34, 35, 44, 11, 43, 45, 14, 15, 16, 17, 18, 46, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300258 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OC(C)C)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 17, 17, 17, 19, 19, 19, 19, 39, 41, 41, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 41, 41, 41, 41, 41, 41, 41, 19, 19, 19, 19] 41 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 32, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300258 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300258 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300258/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300258/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300258 Building REAL300000300259 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300259' /scratch/stefan/7770550/working/building/REAL300000300259 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300259 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300259/0 /scratch/stefan/7770550/working/building/REAL300000300259 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/368 `/scratch/stefan/7770550/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1C) `REAL300000300259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300259 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300259 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 13, 13, 13, 19, 19, 13, 13, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300259 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300259/1 /scratch/stefan/7770550/working/building/REAL300000300259 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/369 `/scratch/stefan/7770550/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1C) `REAL300000300259.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300259 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 15, 17, 20, 20, 20, 20, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 20, 20, 20, 20, 20, 20, 1, 1, 1, 2, 2, 2] 20 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300259 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 20, 20, 17, 13, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300259 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300259 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300259/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300259/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300259 Building REAL300000300260 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300260' /scratch/stefan/7770550/working/building/REAL300000300260 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300260 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300260/0 /scratch/stefan/7770550/working/building/REAL300000300260 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/370 `/scratch/stefan/7770550/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C) `REAL300000300260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300260 none CNC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 17, 30, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 30, 30, 30, 30, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 30 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300260 none CNC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 8, 8, 8, 8, 1, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 30 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 36, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300260 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300260/1 /scratch/stefan/7770550/working/building/REAL300000300260 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/371 `/scratch/stefan/7770550/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C) `REAL300000300260.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300260 none CNC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 21, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 21, 21, 21, 21, 17, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 21 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300260 none CNC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 1, 8, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 8, 8, 8, 8, 1, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 21 rigid atoms, others: [2, 35, 4, 5, 6, 7, 21, 22, 23, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300260 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300260 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300260/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300260/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300260 Building REAL300000300261 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300261' /scratch/stefan/7770550/working/building/REAL300000300261 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300261 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300261/0 /scratch/stefan/7770550/working/building/REAL300000300261 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/372 `/scratch/stefan/7770550/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300261 none CC1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 32, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300261 none CC1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 19, 19, 14, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 11, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300261 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300261/1 /scratch/stefan/7770550/working/building/REAL300000300261 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/373 `/scratch/stefan/7770550/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300261.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300261 none CC1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2] 26 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300261 none CC1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 26, 26, 18, 24, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300261 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300261 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300261/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300261/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300261 Building REAL300000300262 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300262' /scratch/stefan/7770550/working/building/REAL300000300262 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300262 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300262/0 /scratch/stefan/7770550/working/building/REAL300000300262 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/374 `/scratch/stefan/7770550/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(C)C)C=C1) `REAL300000300262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300262 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 23, 28, 31, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 23, 23, 31, 31, 31, 31, 31, 31, 31, 1, 1] 115 rigid atoms, others: [32, 33, 43, 44, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 212 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300262 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 44, 115, 104, 115, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 115, 115, 115, 115, 115, 115, 115, 115, 115, 15, 15] 115 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 467 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300262 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300262 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300262/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300262 Building REAL300000300263 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300263' /scratch/stefan/7770550/working/building/REAL300000300263 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300263 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300263/0 /scratch/stefan/7770550/working/building/REAL300000300263 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/375 `/scratch/stefan/7770550/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N2C=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=N2)C=C1) `REAL300000300263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300263 none CC1=CC=C(N2C=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 22, 23, 24, 25, 38, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300263 none CC1=CC=C(N2C=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 2, 2, 2, 1, 1, 2, 17, 17, 17, 17, 17, 17, 2, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300263 none CC1=CC=C(N2C=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17, 17] 17 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 52 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300263 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300263 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300263/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300263 Building REAL300000300264 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300264' /scratch/stefan/7770550/working/building/REAL300000300264 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300264 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300264/0 /scratch/stefan/7770550/working/building/REAL300000300264 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/376 `/scratch/stefan/7770550/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOC1=CC=C(F)C=C1) `REAL300000300264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300264 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOC1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 183, 201, 201, 201, 201, 201, 156, 87, 34, 87, 87, 16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 156, 34, 34, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 734 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300264 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOC1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 56, 91, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 7, 56, 56, 91, 91, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 570 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300264 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300264 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300264/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300264 Building REAL300000300265 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300265' /scratch/stefan/7770550/working/building/REAL300000300265 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300265 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300265/0 /scratch/stefan/7770550/working/building/REAL300000300265 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/377 `/scratch/stefan/7770550/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CCCC2=C1) `REAL300000300265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300265 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300265 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300265 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300265 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300265/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300265 Building REAL300000300266 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300266' /scratch/stefan/7770550/working/building/REAL300000300266 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300266 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300266/0 /scratch/stefan/7770550/working/building/REAL300000300266 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/378 `/scratch/stefan/7770550/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C)C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300266 none COC1=C(C)C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 2, 2, 2, 15, 15, 15, 15] 15 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300266 none COC1=C(C)C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 9, 13, 15, 15, 15, 15, 15, 1, 1, 1, 3, 3, 3, 2, 2, 2, 1, 9, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2] 15 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 38, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300266 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300266 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300266/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300266 Building REAL300000300267 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300267' /scratch/stefan/7770550/working/building/REAL300000300267 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300267 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300267/0 /scratch/stefan/7770550/working/building/REAL300000300267 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/379 `/scratch/stefan/7770550/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)C3=C2C1=CC=C3) `REAL300000300267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300267 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)C3=C2C1=CC=C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 19, 21, 21, 21, 21, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 13, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300267 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)C3=C2C1=CC=C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300267 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300267/1 /scratch/stefan/7770550/working/building/REAL300000300267 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/380 `/scratch/stefan/7770550/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)C3=C2C1=CC=C3) `REAL300000300267.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300267 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)C3=C2C1=CC=C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 21, 21, 21, 21, 21, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 27, 28, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300267 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)C3=C2C1=CC=C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300267 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300267 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300267/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300267/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300267 Building REAL300000300268 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300268' /scratch/stefan/7770550/working/building/REAL300000300268 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300268 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300268/0 /scratch/stefan/7770550/working/building/REAL300000300268 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/381 `/scratch/stefan/7770550/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300268 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2, 27] 27 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300268 none CC1=C(C(=O)[O-])SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 15, 27, 27, 15, 25, 27, 27, 27, 27, 27, 1, 2, 2, 2, 27, 27, 27, 27, 27, 27, 1] 27 rigid atoms, others: [0, 1, 2, 3, 32, 6, 7, 8, 22] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300268 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300268 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300268/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300268 Building REAL300000300269 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300269' /scratch/stefan/7770550/working/building/REAL300000300269 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300269 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300269/0 /scratch/stefan/7770550/working/building/REAL300000300269 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/382 `/scratch/stefan/7770550/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C(Cl)=C1) `REAL300000300269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300269 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300269 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300269 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300269/1 /scratch/stefan/7770550/working/building/REAL300000300269 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/383 `/scratch/stefan/7770550/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C(Cl)=C1) `REAL300000300269.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300269/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300269 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300269 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300269 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300269 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300269/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300269/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300269 Building REAL300000300270 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300270' /scratch/stefan/7770550/working/building/REAL300000300270 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300270 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300270/0 /scratch/stefan/7770550/working/building/REAL300000300270 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/384 `/scratch/stefan/7770550/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(C#N)=C1) `REAL300000300270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300270 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300270 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300270 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300270/1 /scratch/stefan/7770550/working/building/REAL300000300270 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/385 `/scratch/stefan/7770550/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C#N)=C1) `REAL300000300270.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300270 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300270 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300270 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300270 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300270/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300270/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300270 Building REAL300000300271 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300271' /scratch/stefan/7770550/working/building/REAL300000300271 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300271 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300271/0 /scratch/stefan/7770550/working/building/REAL300000300271 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/386 `/scratch/stefan/7770550/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C) `REAL300000300271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300271 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 9, 14, 19, 19, 19, 19, 9, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 2, 2, 2, 1, 2, 2, 2] 19 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300271 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300271 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300271 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300271/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300271 Building REAL300000300272 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300272' /scratch/stefan/7770550/working/building/REAL300000300272 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300272 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300272/0 /scratch/stefan/7770550/working/building/REAL300000300272 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/387 `/scratch/stefan/7770550/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2COC(=O)C2=C1) `REAL300000300272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300272 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2COC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300272 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2COC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300272 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300272/1 /scratch/stefan/7770550/working/building/REAL300000300272 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/388 `/scratch/stefan/7770550/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2COC(=O)C2=C1) `REAL300000300272.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300272 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2COC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300272 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2COC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300272 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300272 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300272/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300272/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300272 Building REAL300000300273 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300273' /scratch/stefan/7770550/working/building/REAL300000300273 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300273 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300273/0 /scratch/stefan/7770550/working/building/REAL300000300273 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/389 `/scratch/stefan/7770550/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CN=C12) `REAL300000300273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300273 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 2, 2, 2, 21, 21, 21] 21 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300273 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 9, 9, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1, 1, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 20, 21, 22, 23, 24, 25, 38, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300273 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300273/1 /scratch/stefan/7770550/working/building/REAL300000300273 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/390 `/scratch/stefan/7770550/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CN=C12) `REAL300000300273.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300273 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21, 21, 21] 21 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300273 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 9, 13, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 23, 24, 25, 38, 29, 30, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300273 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300273 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300273/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300273/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300273 Building REAL300000300274 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300274' /scratch/stefan/7770550/working/building/REAL300000300274 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300274 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300274/0 /scratch/stefan/7770550/working/building/REAL300000300274 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/391 `/scratch/stefan/7770550/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300274 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300274 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300274 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300274 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300274/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300274 Building REAL300000300275 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300275' /scratch/stefan/7770550/working/building/REAL300000300275 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300275 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300275/0 /scratch/stefan/7770550/working/building/REAL300000300275 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/392 `/scratch/stefan/7770550/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Cl)=C1F) `REAL300000300275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300275 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 17, 27, 27, 27, 27, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300275 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300275 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300275 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300275/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300275 Building REAL300000300276 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300276' /scratch/stefan/7770550/working/building/REAL300000300276 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300276 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300276/0 /scratch/stefan/7770550/working/building/REAL300000300276 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/393 `/scratch/stefan/7770550/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)C(C)=C1) `REAL300000300276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300276 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 10, 17, 23, 23, 23, 23, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 10, 10, 1, 1, 1, 23, 23, 23, 23, 23, 23, 9, 1, 1, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 1] 52 rigid atoms, others: [32, 33, 11, 44, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 147 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300276 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 13, 13, 13, 23, 23, 13, 13, 42, 52, 52, 23, 23, 23, 2, 2, 2, 1, 1, 1, 6, 23, 23, 52, 52, 52, 52, 52, 52, 52, 23, 23, 23, 23] 52 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300276 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300276 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300276/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300276 Building REAL300000300277 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300277' /scratch/stefan/7770550/working/building/REAL300000300277 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300277 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300277/0 /scratch/stefan/7770550/working/building/REAL300000300277 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/394 `/scratch/stefan/7770550/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300277 none COC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 39, 39, 39, 39, 39, 39, 1, 1, 1, 2, 2, 2] 39 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300277 none COC1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 39, 39, 25, 36, 39, 39, 39, 39, 39, 3, 3, 3, 1, 1, 1, 39, 39, 39, 39, 39, 39] 39 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300277 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300277 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300277/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300277 Building REAL300000300278 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300278' /scratch/stefan/7770550/working/building/REAL300000300278 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300278 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300278/0 /scratch/stefan/7770550/working/building/REAL300000300278 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/395 `/scratch/stefan/7770550/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12) `REAL300000300278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300278 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21] 21 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300278 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 9, 9, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 41, 20, 21, 22, 23, 24, 25, 38, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300278 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300278/1 /scratch/stefan/7770550/working/building/REAL300000300278 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/396 `/scratch/stefan/7770550/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12) `REAL300000300278.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300278 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21] 21 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300278 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 9, 13, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 20, 21, 22, 23, 24, 25, 38, 29, 30, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300278 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300278 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300278/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300278/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300278 Building REAL300000300279 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300279' /scratch/stefan/7770550/working/building/REAL300000300279 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300279 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300279/0 /scratch/stefan/7770550/working/building/REAL300000300279 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/397 `/scratch/stefan/7770550/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300279 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300279 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300279 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300279/1 /scratch/stefan/7770550/working/building/REAL300000300279 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/398 `/scratch/stefan/7770550/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300279.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300279 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300279 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300279 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300279 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300279/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300279/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300279 Building REAL300000300280 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300280' /scratch/stefan/7770550/working/building/REAL300000300280 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300280 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300280/0 /scratch/stefan/7770550/working/building/REAL300000300280 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/399 `/scratch/stefan/7770550/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1C) `REAL300000300280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300280 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300280 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 13, 13, 13, 19, 19, 13, 13, 19, 19, 19, 2, 2, 2, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300280 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300280 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300280/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300280 Building REAL300000300281 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300281' /scratch/stefan/7770550/working/building/REAL300000300281 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300281 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300281/0 /scratch/stefan/7770550/working/building/REAL300000300281 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/400 `/scratch/stefan/7770550/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=C(Cl)C=C1Cl) `REAL300000300281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300281 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 13, 13, 17, 17, 17, 17, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300281 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300281 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300281 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300281/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300281 Building REAL300000300282 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300282' /scratch/stefan/7770550/working/building/REAL300000300282 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300282 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300282/0 /scratch/stefan/7770550/working/building/REAL300000300282 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/401 `/scratch/stefan/7770550/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300282 none CC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 26, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 26] 26 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300282 none CC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 26, 26, 20, 20, 26, 26, 26, 26, 26, 1, 2, 2, 2, 1, 1, 26, 26, 26, 26, 26, 26, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300282 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300282/1 /scratch/stefan/7770550/working/building/REAL300000300282 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/402 `/scratch/stefan/7770550/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300282.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300282 none CC1=CC=C(F)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 19, 29, 29, 29, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 7, 1, 1, 1, 2, 2, 2, 29] 29 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 34, 33, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300282 none CC1=CC=C(F)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 29, 29, 17, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 1, 1, 17, 29, 29, 29, 29, 29, 29, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300282 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300282 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300282/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300282/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300282 Building REAL300000300283 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300283' /scratch/stefan/7770550/working/building/REAL300000300283 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300283 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300283/0 /scratch/stefan/7770550/working/building/REAL300000300283 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/403 `/scratch/stefan/7770550/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300283 none CC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 33, 32, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300283 none CC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 19, 19, 11, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 11, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300283 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300283/1 /scratch/stefan/7770550/working/building/REAL300000300283 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/404 `/scratch/stefan/7770550/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300283.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300283 none CC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2] 26 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300283 none CC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 26, 26, 18, 22, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300283 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300283 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300283/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300283/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300283 Building REAL300000300284 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300284' /scratch/stefan/7770550/working/building/REAL300000300284 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300284 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300284/0 /scratch/stefan/7770550/working/building/REAL300000300284 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/405 `/scratch/stefan/7770550/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC=C1[N+](=O)[O-]) `REAL300000300284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300284 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 5, 9, 9, 9, 9, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1] 9 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300284 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300284 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300284 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300284/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300284 Building REAL300000300285 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300285' /scratch/stefan/7770550/working/building/REAL300000300285 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300285 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300285/0 /scratch/stefan/7770550/working/building/REAL300000300285 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/406 `/scratch/stefan/7770550/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1F)NC(=O)CC2) `REAL300000300285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300285 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1F)NC(=O)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 19, 24, 24, 24, 24, 24, 14, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300285 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1F)NC(=O)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 24, 24, 11, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300285 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300285/1 /scratch/stefan/7770550/working/building/REAL300000300285 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/407 `/scratch/stefan/7770550/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1F)NC(=O)CC2) `REAL300000300285.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300285 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1F)NC(=O)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 17, 18, 28, 28, 28, 28, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 17, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300285 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1F)NC(=O)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 28, 28, 10, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 1, 1, 1, 6, 28, 28, 28, 28, 28, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300285 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300285 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300285/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300285/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300285 Building REAL300000300286 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300286' /scratch/stefan/7770550/working/building/REAL300000300286 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300286 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300286/0 /scratch/stefan/7770550/working/building/REAL300000300286 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/408 `/scratch/stefan/7770550/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1C(F)(F)F) `REAL300000300286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300286 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 5, 8, 12, 12, 12, 12, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 1, 1, 1] 12 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300286 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300286 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300286/1 /scratch/stefan/7770550/working/building/REAL300000300286 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/409 `/scratch/stefan/7770550/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1C(F)(F)F) `REAL300000300286.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300286 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1] 11 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300286 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300286 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300286 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300286/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300286/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300286 Building REAL300000300287 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300287' /scratch/stefan/7770550/working/building/REAL300000300287 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300287 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300287/0 /scratch/stefan/7770550/working/building/REAL300000300287 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/410 `/scratch/stefan/7770550/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)N(C)C)=C1) `REAL300000300287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300287 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)N(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1] 34 rigid atoms, others: [32, 33, 34, 41, 11, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300287 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)N(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 34, 34, 34, 34, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 34, 34, 34, 34, 34, 34, 17] 34 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300287 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300287/1 /scratch/stefan/7770550/working/building/REAL300000300287 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/411 `/scratch/stefan/7770550/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)N(C)C)=C1) `REAL300000300287.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300287 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)N(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 16, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1] 25 rigid atoms, others: [32, 33, 40, 11, 14, 15, 16, 17, 18, 19, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 51 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300287 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)N(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 25, 25, 25, 25, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 25, 25, 25, 25, 25, 25, 17] 25 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300287 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300287 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300287/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300287/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300287 Building REAL300000300288 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300288' /scratch/stefan/7770550/working/building/REAL300000300288 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300288 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300288/0 /scratch/stefan/7770550/working/building/REAL300000300288 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/412 `/scratch/stefan/7770550/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC2CCCC2)C=C1) `REAL300000300288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300288 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 5, 9, 14, 14, 14, 14, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 1, 1, 14, 14, 14, 14, 14, 14, 5, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 77 rigid atoms, others: [33, 34, 11, 44, 45, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300288 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 53, 77, 77, 77, 77, 14, 14, 2, 2, 2, 1, 1, 1, 6, 14, 14, 77, 77, 77, 77, 77, 77, 77, 77, 77, 14, 14] 77 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 204 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300288 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 44, 77, 77, 77, 77, 77, 44, 17, 17, 17, 17, 16, 17, 17, 6, 1, 1, 1, 1, 1, 1, 17, 17, 77, 77, 77, 77, 77, 77, 44, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 77 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 339 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300288 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300288 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300288/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300288 Building REAL300000300289 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300289' /scratch/stefan/7770550/working/building/REAL300000300289 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300289 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300289/0 /scratch/stefan/7770550/working/building/REAL300000300289 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/413 `/scratch/stefan/7770550/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCCC(C)C)C=C1) `REAL300000300289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300289 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCCC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 33, 36, 36, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 24, 24, 33, 33, 36, 36, 36, 36, 36, 36, 36, 1, 1] 160 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 46, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 219 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300289 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCCC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 60, 111, 160, 160, 160, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 111, 111, 160, 160, 160, 160, 160, 160, 160, 160, 160, 15, 15] 160 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 635 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300289 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300289 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300289/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300289 Building REAL300000300290 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300290' /scratch/stefan/7770550/working/building/REAL300000300290 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300290 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300290/0 /scratch/stefan/7770550/working/building/REAL300000300290 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/414 `/scratch/stefan/7770550/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300290 none COC(=O)COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 66, 124, 19, 9, 5, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 124, 124, 124, 66, 66, 9, 9, 5, 1, 1, 1, 2, 2, 2, 9, 9] 124 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 459 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300290 none COC(=O)COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 15, 52, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 9, 9, 7, 9, 9, 9, 9, 9, 9, 1, 1, 52, 52, 52, 15, 15, 1, 1, 5, 9, 9, 9, 9, 9, 9, 1, 1] 124 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 40, 41, 24, 25, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 184 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300290 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300290 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300290/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300290 Building REAL300000300291 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300291' /scratch/stefan/7770550/working/building/REAL300000300291 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300291 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300291/0 /scratch/stefan/7770550/working/building/REAL300000300291 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/415 `/scratch/stefan/7770550/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC(C(=O)[O-])=C1) `REAL300000300291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300291 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 7, 13, 13, 13, 13, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300291 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 5, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300291 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300291/1 /scratch/stefan/7770550/working/building/REAL300000300291 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/416 `/scratch/stefan/7770550/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC(C(=O)[O-])=C1) `REAL300000300291.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300291 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 12, 13, 13, 13, 13, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300291 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300291 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300291 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300291/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300291/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300291 Building REAL300000300292 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300292' /scratch/stefan/7770550/working/building/REAL300000300292 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300292 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300292/0 /scratch/stefan/7770550/working/building/REAL300000300292 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/417 `/scratch/stefan/7770550/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC(C)=C1Cl) `REAL300000300292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300292 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 23, 27, 39, 39, 39, 39, 23, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 1, 1, 2, 2, 2] 39 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300292 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 39, 39, 39, 33, 39, 39, 39, 39, 2, 2, 2, 1, 1, 1, 39, 35, 39, 39, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300292 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300292 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300292/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300292 Building REAL300000300293 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300293' /scratch/stefan/7770550/working/building/REAL300000300293 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300293 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300293/0 /scratch/stefan/7770550/working/building/REAL300000300293 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/418 `/scratch/stefan/7770550/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC(C(=O)[O-])=C1OC) `REAL300000300293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300293 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC(C(=O)[O-])=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 11, 11, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 11, 19, 19, 11, 11, 19, 27, 27, 27, 11, 5, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19] 31 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300293 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC(C(=O)[O-])=C1OC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 3, 3, 5, 11, 11, 5, 9, 11, 11, 11, 11, 11, 1, 1, 1, 3, 3, 1, 1, 2, 3, 3, 3, 1, 5, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2] 31 rigid atoms, others: [1, 2, 3, 4, 5, 38, 19, 20, 21, 24, 25, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300293 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300293 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300293/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300293 Building REAL300000300294 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300294' /scratch/stefan/7770550/working/building/REAL300000300294 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300294 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300294/0 /scratch/stefan/7770550/working/building/REAL300000300294 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/419 `/scratch/stefan/7770550/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300294 none CC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 17, 19, 19, 30, 30, 30, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 17, 30, 30, 30, 19, 7, 1, 1, 1, 2, 2, 2] 30 rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300294 none CC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 5, 5, 5, 11, 19, 19, 11, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 3, 3, 3, 1, 11, 19, 19, 19, 19, 19, 19] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 9, 10, 11, 28, 29] set([6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300294 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300294/1 /scratch/stefan/7770550/working/building/REAL300000300294 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/420 `/scratch/stefan/7770550/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300294.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300294 none CC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 19, 19, 25, 25, 25, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 13, 25, 25, 25, 19, 1, 1, 1, 2, 2, 2] 25 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300294 none CC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7, 11, 19, 19, 11, 13, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 3, 3, 3, 1, 19, 19, 19, 19, 19, 19] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 9, 10, 11, 28, 29] set([6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300294 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300294 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300294/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300294/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300294 Building REAL300000300295 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300295' /scratch/stefan/7770550/working/building/REAL300000300295 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300295 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300295/0 /scratch/stefan/7770550/working/building/REAL300000300295 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/421 `/scratch/stefan/7770550/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-]) `REAL300000300295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300295 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 25, 25, 25, 25, 25, 13, 13, 5, 1, 1, 1, 2, 2, 2, 13] 25 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300295 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 13, 13, 5, 9, 13, 13, 13, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 5, 13, 13, 13, 13, 13, 13, 1] 25 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300295 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300295 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300295/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300295 Building REAL300000300296 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300296' /scratch/stefan/7770550/working/building/REAL300000300296 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300296 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300296/0 /scratch/stefan/7770550/working/building/REAL300000300296 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/422 `/scratch/stefan/7770550/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300296 none COC(=O)CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 101, 201, 53, 21, 9, 5, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 201, 201, 201, 101, 101, 53, 53, 9, 9, 5, 1, 1, 1, 2, 2, 2, 9, 9] 201 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 809 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300296 none COC(=O)CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 25, 87, 11, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 9, 9, 7, 9, 9, 9, 9, 9, 9, 1, 1, 87, 87, 87, 25, 25, 11, 11, 1, 1, 5, 9, 9, 9, 9, 9, 9, 1, 1] 201 rigid atoms, others: [34, 35, 6, 7, 8, 9, 10, 11, 44, 43, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 299 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300296 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300296 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300296/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300296 Building REAL300000300297 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300297' /scratch/stefan/7770550/working/building/REAL300000300297 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300297 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300297/0 /scratch/stefan/7770550/working/building/REAL300000300297 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/423 `/scratch/stefan/7770550/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)C=CS1) `REAL300000300297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300297 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 29, 29, 39, 39, 39, 39, 29, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 1, 1] 39 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300297 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 1, 39, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300297 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300297 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300297/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300297 Building REAL300000300298 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300298' /scratch/stefan/7770550/working/building/REAL300000300298 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300298 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300298/0 /scratch/stefan/7770550/working/building/REAL300000300298 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/424 `/scratch/stefan/7770550/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1O) `REAL300000300298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300298 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', '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, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 17, 55, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 55, 55, 55, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 34] 110 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300298 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', '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, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 6, 6, 6, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1, 2] 110 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 36, 28, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300298 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300298 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300298/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300298 Building REAL300000300299 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300299' /scratch/stefan/7770550/working/building/REAL300000300299 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300299 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300299/0 /scratch/stefan/7770550/working/building/REAL300000300299 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/425 `/scratch/stefan/7770550/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300299 none CC(=O)NCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 73, 32, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 140, 140, 140, 140, 73, 73, 32, 32, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 140 rigid atoms, others: [37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44]) total number of confs: 556 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300299 none CC(=O)NCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 8, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 18, 18, 18, 18, 8, 8, 4, 4, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 140 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 10, 43, 44, 24, 25] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300299 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300299 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300299/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300299 Building REAL300000300300 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300300' /scratch/stefan/7770550/working/building/REAL300000300300 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300300 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300300/0 /scratch/stefan/7770550/working/building/REAL300000300300 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/426 `/scratch/stefan/7770550/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1[N+](=O)[O-]) `REAL300000300300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300300 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 5, 5, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 1, 1, 1] 11 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300300 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300300 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300300 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300300/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300300 Building REAL300000300301 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300301' /scratch/stefan/7770550/working/building/REAL300000300301 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300301 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300301/0 /scratch/stefan/7770550/working/building/REAL300000300301 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/427 `/scratch/stefan/7770550/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CNC(C)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300301 none COC1=CC=C(CNC(C)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 5, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 51, 51, 51, 51, 51, 51, 146, 201, 201, 201, 51, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 73, 73, 73, 51, 51, 146, 146, 201, 201, 201, 201, 51, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 739 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300301 none COC1=CC=C(CNC(C)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 5, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 8, 36, 36, 36, 1, 1, 1, 7, 7, 7, 25, 51, 51, 25, 45, 51, 51, 51, 51, 51, 4, 4, 4, 1, 1, 8, 8, 36, 36, 36, 36, 1, 51, 51, 51, 51, 51, 51] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 13, 38, 30, 31] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300301 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300301/1 /scratch/stefan/7770550/working/building/REAL300000300301 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/428 `/scratch/stefan/7770550/working/3D/428' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CNC(C)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300301.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300301/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300301 none COC1=CC=C(CNC(C)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 5, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [43, 35, 35, 35, 35, 35, 35, 127, 187, 187, 187, 35, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 35, 35, 127, 127, 187, 187, 187, 187, 35, 5, 1, 1, 1, 2, 2, 2] 187 rigid atoms, others: [40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45]) total number of confs: 669 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300301 none COC1=CC=C(CNC(C)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 5, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 35, 35, 35, 1, 1, 1, 7, 7, 7, 21, 35, 35, 21, 33, 35, 35, 35, 35, 35, 3, 3, 3, 1, 1, 9, 9, 35, 35, 35, 35, 1, 21, 35, 35, 35, 35, 35, 35] 187 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 13, 38, 30, 31] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300301 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300301 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300301/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300301/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300301 Building REAL300000300302 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300302' /scratch/stefan/7770550/working/building/REAL300000300302 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300302 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300302/0 /scratch/stefan/7770550/working/building/REAL300000300302 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/429 `/scratch/stefan/7770550/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCCC2) `REAL300000300302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300302 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 7, 11, 11, 11, 11, 7, 4, 1, 4, 4, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300302 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300302 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300302 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300302/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300302 Building REAL300000300303 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300303' /scratch/stefan/7770550/working/building/REAL300000300303 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300303 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300303/0 /scratch/stefan/7770550/working/building/REAL300000300303 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/430 `/scratch/stefan/7770550/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C(C)C) `REAL300000300303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300303 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 6, 7, 7, 7, 7, 7, 5, 3, 1, 3, 3, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2] 7 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300303 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300303 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300303 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300303/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300303 Building REAL300000300304 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300304' /scratch/stefan/7770550/working/building/REAL300000300304 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300304 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300304/0 /scratch/stefan/7770550/working/building/REAL300000300304 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/431 `/scratch/stefan/7770550/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2=CC=CC=C2)C=C1) `REAL300000300304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300304 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 3, 3, 1, 3, 3, 1, 1] 15 rigid atoms, others: [33, 34, 40, 41, 11, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300304 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300304 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 15, 15, 15, 15, 15, 9, 3, 3, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 15, 15, 15, 15, 15, 9, 3, 3, 1, 1, 1, 1, 1, 3, 3] 15 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41]) total number of confs: 69 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300304 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300304 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300304/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300304 Building REAL300000300305 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300305' /scratch/stefan/7770550/working/building/REAL300000300305 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300305 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300305/0 /scratch/stefan/7770550/working/building/REAL300000300305 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/432 `/scratch/stefan/7770550/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(C)NN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300305 none CCOC(=O)C1=C(C)NN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 195, 81, 195, 81, 81, 81, 81, 81, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 81, 81, 81, 81, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 526 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300305 none CCOC(=O)C1=C(C)NN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 20, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 33, 81, 81, 33, 44, 81, 81, 81, 81, 81, 38, 38, 38, 38, 38, 2, 2, 2, 1, 81, 81, 81, 81, 81, 81] 201 rigid atoms, others: [33, 3, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300305 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300305 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300305/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300305 Building REAL300000300306 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300306' /scratch/stefan/7770550/working/building/REAL300000300306 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300306 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300306/0 /scratch/stefan/7770550/working/building/REAL300000300306 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/433 `/scratch/stefan/7770550/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCNC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300306 none C=CCNC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 55, 55, 17, 55, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 125, 125, 125, 125, 125, 55, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 125 rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 519 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300306 none C=CCNC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [39, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 39, 39, 39, 25, 25, 5, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 125 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 25, 42] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300306 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300306/1 /scratch/stefan/7770550/working/building/REAL300000300306 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/434 `/scratch/stefan/7770550/working/3D/434' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCNC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300306.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300306 none C=CCNC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 39, 39, 19, 39, 19, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 91, 91, 91, 91, 91, 39, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19] 91 rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300306 none C=CCNC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [31, 19, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 11, 17, 19, 19, 19, 19, 19, 1, 31, 31, 31, 19, 19, 5, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1] 91 rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 41, 25] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300306 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300306 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300306/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300306/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300306 Building REAL300000300307 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300307' /scratch/stefan/7770550/working/building/REAL300000300307 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300307 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300307/0 /scratch/stefan/7770550/working/building/REAL300000300307 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/435 `/scratch/stefan/7770550/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1) `REAL300000300307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300307 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 19, 29, 29, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 8, 1, 1, 1, 2, 2, 2, 29, 29, 29, 29] 29 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 139 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300307 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 29, 29, 15, 19, 29, 29, 29, 29, 29, 1, 1, 1, 3, 3, 3, 1, 1, 13, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1] 29 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300307 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300307 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300307/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300307 Building REAL300000300308 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300308' /scratch/stefan/7770550/working/building/REAL300000300308 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300308 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300308/0 /scratch/stefan/7770550/working/building/REAL300000300308 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/436 `/scratch/stefan/7770550/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300308 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19] 19 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300308 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 19, 19, 5, 9, 19, 19, 19, 19, 19, 1, 1, 1, 3, 3, 3, 1, 2, 2, 2, 5, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 38, 21, 22, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300308 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300308 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300308/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300308 Building REAL300000300309 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300309' /scratch/stefan/7770550/working/building/REAL300000300309 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300309 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300309/0 /scratch/stefan/7770550/working/building/REAL300000300309 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/437 `/scratch/stefan/7770550/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)NC2CC2)=C1) `REAL300000300309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300309 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)NC2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 23, 9, 17, 23, 23, 23, 23, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 1, 23, 23, 23, 23, 23, 23, 9, 1, 1, 1, 6, 18, 18, 18, 18, 18, 1] 66 rigid atoms, others: [33, 34, 35, 42, 11, 14, 15, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300309 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)NC2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 23, 23, 23, 23, 23, 60, 60, 60, 66, 66, 23, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 60, 66, 66, 66, 66, 66, 23] 66 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300309 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)NC2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 42, 66, 66, 66, 66, 66, 42, 26, 18, 26, 26, 18, 9, 18, 18, 5, 5, 5, 1, 1, 1, 1, 18, 66, 66, 66, 66, 66, 66, 42, 9, 18, 18, 5, 1, 1, 1, 1, 1, 18] 66 rigid atoms, others: [37, 38, 39, 40, 41, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 325 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300309 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300309/1 /scratch/stefan/7770550/working/building/REAL300000300309 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/438 `/scratch/stefan/7770550/working/3D/438' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)NC2CC2)=C1) `REAL300000300309.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300309 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)NC2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 23, 23, 9, 17, 23, 23, 23, 23, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 5, 13, 13, 13, 13, 13, 1] 45 rigid atoms, others: [32, 33, 34, 41, 11, 14, 15, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300309 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)NC2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 23, 23, 23, 23, 23, 43, 43, 43, 45, 45, 23, 2, 2, 2, 1, 1, 1, 23, 23, 23, 43, 45, 45, 45, 45, 45, 23] 45 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300309 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)NC2CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 33, 45, 45, 45, 45, 45, 33, 21, 13, 21, 21, 13, 7, 13, 13, 5, 5, 5, 1, 1, 1, 1, 13, 45, 45, 45, 45, 45, 45, 7, 13, 13, 5, 1, 1, 1, 1, 1, 13] 45 rigid atoms, others: [36, 37, 38, 39, 40, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300309 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300309 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300309/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300309/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300309 Building REAL300000300310 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300310' /scratch/stefan/7770550/working/building/REAL300000300310 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000300310 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300310/0 /scratch/stefan/7770550/working/building/REAL300000300310 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/439 `/scratch/stefan/7770550/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300310 none CC1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 28, 28, 28, 28, 28, 28, 56, 1, 1, 1, 2, 2, 2, 28] 56 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300310 none CC1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 28, 28, 16, 16, 28, 28, 28, 28, 28, 1, 2, 2, 2, 1, 1, 2, 28, 28, 28, 28, 28, 28, 1] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300310 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300310/1 /scratch/stefan/7770550/working/building/REAL300000300310 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/440 `/scratch/stefan/7770550/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(O)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300310.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300310 none CC1=CC=C(O)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 26, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 52, 5, 1, 1, 1, 2, 2, 2, 26] 52 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300310 none CC1=CC=C(O)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 26, 26, 17, 26, 26, 26, 26, 26, 26, 1, 2, 2, 2, 1, 1, 2, 17, 26, 26, 26, 26, 26, 26, 1] 52 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300310 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `2' /scratch/stefan/7770550/working/building/REAL300000300310/2 /scratch/stefan/7770550/working/building/REAL300000300310 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 2 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/441 `/scratch/stefan/7770550/working/3D/441' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([O-])C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300310.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000300310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300310/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300310 none CC1=CC=C([O-])C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 7, 1, 1, 1, 2, 2, 2, 11] 11 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 34, 33, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300310 none CC1=CC=C([O-])C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 11, 11, 7, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 1, 1, 5, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300310 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300310 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 2: /scratch/stefan/7770550/working/building/REAL300000300310/2.* 1: /scratch/stefan/7770550/working/building/REAL300000300310/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300310/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300310 Building REAL300000300311 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300311' /scratch/stefan/7770550/working/building/REAL300000300311 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300311 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300311/0 /scratch/stefan/7770550/working/building/REAL300000300311 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/442 `/scratch/stefan/7770550/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300311 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 2, 2, 2] 21 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300311 none CCC1=CC=C(C(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 9, 21, 21, 10, 17, 21, 21, 21, 21, 21, 4, 4, 4, 4, 4, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 30, 31] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300311 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300311 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300311/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300311 Building REAL300000300312 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300312' /scratch/stefan/7770550/working/building/REAL300000300312 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300312 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300312/0 /scratch/stefan/7770550/working/building/REAL300000300312 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/443 `/scratch/stefan/7770550/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)N=C2C=CC=CN21) `REAL300000300312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300312 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)N=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 27, 39, 39, 39, 39, 39, 23, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1] 39 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300312 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)N=C2C=CC=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 17, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 1, 39, 39, 39, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300312 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300312 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300312/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300312 Building REAL300000300313 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300313' /scratch/stefan/7770550/working/building/REAL300000300313 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300313 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300313/0 /scratch/stefan/7770550/working/building/REAL300000300313 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/444 `/scratch/stefan/7770550/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1)N(C)C1=C2C=CC=C1) `REAL300000300313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300313 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1)N(C)C1=C2C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 13, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300313 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1)N(C)C1=C2C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300313 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300313/1 /scratch/stefan/7770550/working/building/REAL300000300313 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/445 `/scratch/stefan/7770550/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1)N(C)C1=C2C=CC=C1) `REAL300000300313.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300313 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1)N(C)C1=C2C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300313 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1)N(C)C1=C2C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300313 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300313 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300313/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300313/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300313 Building REAL300000300314 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300314' /scratch/stefan/7770550/working/building/REAL300000300314 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300314 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300314/0 /scratch/stefan/7770550/working/building/REAL300000300314 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/446 `/scratch/stefan/7770550/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300314 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [59, 49, 49, 49, 31, 49, 49, 63, 69, 69, 49, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 59, 59, 59, 49, 49, 63, 63, 49, 1, 1, 1, 2, 2, 2] 69 rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300314 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 7, 7, 21, 49, 49, 21, 21, 49, 49, 49, 49, 49, 3, 3, 3, 1, 1, 2, 2, 1, 49, 49, 49, 49, 49, 49] 69 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 10, 11, 12, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300314 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300314/1 /scratch/stefan/7770550/working/building/REAL300000300314 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/447 `/scratch/stefan/7770550/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300314.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300314 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [37, 35, 35, 35, 25, 35, 35, 49, 49, 49, 35, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 35, 35, 49, 49, 35, 7, 1, 1, 1, 2, 2, 2] 49 rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300314 none COC1=CC=C(CC(=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 7, 7, 7, 15, 35, 35, 15, 27, 35, 35, 35, 35, 35, 4, 4, 4, 1, 1, 2, 2, 1, 15, 35, 35, 35, 35, 35, 35] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 10, 11, 12, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300314 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300314 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300314/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300314/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300314 Building REAL300000300315 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300315' /scratch/stefan/7770550/working/building/REAL300000300315 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300315 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300315/0 /scratch/stefan/7770550/working/building/REAL300000300315 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/448 `/scratch/stefan/7770550/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C(=O)[O-])=C1) `REAL300000300315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300315 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1] 9 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 32, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300315 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300315 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300315 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300315/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300315 Building REAL300000300316 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300316' /scratch/stefan/7770550/working/building/REAL300000300316 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300316 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300316/0 /scratch/stefan/7770550/working/building/REAL300000300316 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/449 `/scratch/stefan/7770550/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300316 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 44, 66, 44, 44, 44, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 66, 66, 66, 44, 44, 1, 1, 1, 2, 2, 2] 66 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300316 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [9, 9, 1, 9, 1, 1, 1, 1, 1, 6, 6, 6, 25, 44, 44, 25, 39, 44, 44, 44, 44, 44, 1, 10, 9, 9, 1, 1, 44, 44, 44, 44, 44, 44] 66 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300316 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300316 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300316/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300316 Building REAL300000300317 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300317' /scratch/stefan/7770550/working/building/REAL300000300317 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300317 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300317/0 /scratch/stefan/7770550/working/building/REAL300000300317 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/450 `/scratch/stefan/7770550/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCC2) `REAL300000300317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300317 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 8, 14, 14, 14, 14, 14, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300317 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300317 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300317 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300317/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300317 Building REAL300000300318 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300318' /scratch/stefan/7770550/working/building/REAL300000300318 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300318 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300318/0 /scratch/stefan/7770550/working/building/REAL300000300318 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/451 `/scratch/stefan/7770550/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(S(C)(=O)=O)=C1) `REAL300000300318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300318 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(S(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 5, 5, 5, 1] 33 rigid atoms, others: [32, 33, 37, 11, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300318 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(S(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 15, 17, 17, 17, 33, 33, 33, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 33, 33, 33, 17] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300318 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300318/1 /scratch/stefan/7770550/working/building/REAL300000300318 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/452 `/scratch/stefan/7770550/working/3D/452' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(S(C)(=O)=O)=C1) `REAL300000300318.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300318 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(S(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 9, 17, 18, 18, 18, 18, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 18, 18, 18, 18, 18, 18, 1, 1, 5, 5, 5, 1] 26 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 19, 20, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300318 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C(S(C)(=O)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 14, 5, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 10, 10, 10, 18, 18, 10, 18, 18, 18, 26, 26, 26, 18, 2, 2, 2, 1, 1, 1, 18, 18, 26, 26, 26, 18] 26 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300318 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300318 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300318/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300318/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300318 Building REAL300000300319 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300319' /scratch/stefan/7770550/working/building/REAL300000300319 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300319 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300319/0 /scratch/stefan/7770550/working/building/REAL300000300319 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/453 `/scratch/stefan/7770550/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300319 none CC1=CC([N+](=O)[O-])=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11] 11 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300319 none CC1=CC([N+](=O)[O-])=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 11, 11, 5, 7, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 35, 22, 23, 24, 28] set([5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300319 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300319 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300319/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300319 Building REAL300000300320 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300320' /scratch/stefan/7770550/working/building/REAL300000300320 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300320 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300320/0 /scratch/stefan/7770550/working/building/REAL300000300320 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/454 `/scratch/stefan/7770550/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1COC2=O) `REAL300000300320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300320 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1COC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 13, 23, 23, 23, 23, 23, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 13, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300320 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1COC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300320 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300320/1 /scratch/stefan/7770550/working/building/REAL300000300320 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/455 `/scratch/stefan/7770550/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1COC2=O) `REAL300000300320.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300320 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1COC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 23, 23, 23, 23, 23, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300320 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1COC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 5, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300320 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300320 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300320/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300320/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300320 Building REAL300000300321 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300321' /scratch/stefan/7770550/working/building/REAL300000300321 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300321 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300321/0 /scratch/stefan/7770550/working/building/REAL300000300321 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/456 `/scratch/stefan/7770550/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=C(F)C=C1F) `REAL300000300321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300321 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 15, 21, 21, 21, 21, 15, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300321 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 21, 21, 21, 20, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300321 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300321 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300321/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300321 Building REAL300000300322 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300322' /scratch/stefan/7770550/working/building/REAL300000300322 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300322 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300322/0 /scratch/stefan/7770550/working/building/REAL300000300322 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/457 `/scratch/stefan/7770550/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300322 none CC(=O)NCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 98, 98, 47, 47, 47, 47, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 151, 151, 151, 151, 98, 98, 98, 98, 47, 47, 1, 1, 1, 2, 2, 2] 151 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 535 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300322 none CC(=O)NCCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 11, 9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 47, 47, 23, 43, 47, 47, 47, 47, 47, 1, 30, 30, 30, 29, 11, 11, 8, 8, 1, 1, 47, 47, 47, 47, 47, 47] 151 rigid atoms, others: [33, 34, 5, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300322 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300322 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300322/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300322 Building REAL300000300323 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300323' /scratch/stefan/7770550/working/building/REAL300000300323 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300323 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300323/0 /scratch/stefan/7770550/working/building/REAL300000300323 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/458 `/scratch/stefan/7770550/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300323 none CC(=O)NC(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 136, 57, 136, 57, 57, 57, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 139, 139, 139, 139, 136, 136, 136, 136, 57, 57, 1, 1, 1, 2, 2, 2] 139 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300323 none CC(=O)NC(C)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 6, 25, 57, 57, 40, 46, 57, 57, 57, 57, 57, 1, 22, 22, 22, 22, 13, 13, 13, 13, 1, 1, 57, 57, 57, 57, 57, 57] 139 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 24] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300323 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300323 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300323/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300323 Building REAL300000300324 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300324' /scratch/stefan/7770550/working/building/REAL300000300324 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300324 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300324/0 /scratch/stefan/7770550/working/building/REAL300000300324 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/459 `/scratch/stefan/7770550/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])O1) `REAL300000300324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300324 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19] 19 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 32, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300324 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 13, 19, 19, 13, 13, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300324 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300324/1 /scratch/stefan/7770550/working/building/REAL300000300324 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/460 `/scratch/stefan/7770550/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])O1) `REAL300000300324.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300324 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300324 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 33, 17, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300324 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300324 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300324/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300324/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300324 Building REAL300000300325 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300325' /scratch/stefan/7770550/working/building/REAL300000300325 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300325 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300325/0 /scratch/stefan/7770550/working/building/REAL300000300325 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/461 `/scratch/stefan/7770550/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2NC=CC=C12) `REAL300000300325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300325 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 21, 21, 29, 29, 29, 29, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300325 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300325 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300325 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300325/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300325 Building REAL300000300326 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300326' /scratch/stefan/7770550/working/building/REAL300000300326 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300326 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300326/0 /scratch/stefan/7770550/working/building/REAL300000300326 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/462 `/scratch/stefan/7770550/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300326 none COC(=O)C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 47, 69, 47, 47, 47, 47, 47, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 47, 69, 69, 69, 47, 47, 1, 1, 1, 2, 2, 2, 47] 69 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300326 none COC(=O)C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 47, 47, 23, 29, 47, 47, 47, 47, 47, 1, 12, 12, 12, 1, 1, 47, 47, 47, 47, 47, 47, 1] 69 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 36, 28, 29] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300326 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300326 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300326/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300326 Building REAL300000300327 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300327' /scratch/stefan/7770550/working/building/REAL300000300327 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300327 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300327/0 /scratch/stefan/7770550/working/building/REAL300000300327 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/463 `/scratch/stefan/7770550/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300327 none CCOC1=CC=C(C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 80, 48, 48, 48, 48, 48, 48, 48, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 82, 82, 82, 82, 82, 48, 48, 48, 48, 48, 48, 1, 1, 1, 2, 2, 2] 82 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300327 none CCOC1=CC=C(C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 48, 48, 22, 22, 48, 48, 48, 48, 48, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 1, 48, 48, 48, 48, 48, 48] 82 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 29, 30] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300327 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300327/1 /scratch/stefan/7770550/working/building/REAL300000300327 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/464 `/scratch/stefan/7770550/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300327.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300327 none CCOC1=CC=C(C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 73, 49, 49, 49, 49, 49, 49, 49, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 49, 49, 49, 49, 49, 49, 7, 1, 1, 1, 2, 2, 2] 75 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 169 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300327 none CCOC1=CC=C(C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 49, 49, 25, 41, 49, 49, 49, 49, 49, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 1, 25, 49, 49, 49, 49, 49, 49] 75 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 29, 30] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 287 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300327 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300327 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300327/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300327/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300327 Building REAL300000300328 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300328' /scratch/stefan/7770550/working/building/REAL300000300328 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300328 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300328/0 /scratch/stefan/7770550/working/building/REAL300000300328 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/465 `/scratch/stefan/7770550/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(C(F)(F)F)=C1) `REAL300000300328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300328 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300328 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300328 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300328 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300328/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300328 Building REAL300000300329 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300329' /scratch/stefan/7770550/working/building/REAL300000300329 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300329 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300329/0 /scratch/stefan/7770550/working/building/REAL300000300329 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/466 `/scratch/stefan/7770550/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300329 none CCN(CC)C(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [42, 24, 24, 24, 40, 19, 24, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 42, 42, 42, 42, 42, 40, 40, 40, 40, 40, 19, 19, 7, 1, 1, 1, 2, 2, 2, 19, 19] 74 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47]) total number of confs: 281 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300329 none CCN(CC)C(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 6, 6, 7, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 17, 17, 19, 19, 19, 19, 19, 1, 1, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1] 74 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 46, 47, 25, 26, 5] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300329 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300329/1 /scratch/stefan/7770550/working/building/REAL300000300329 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/467 `/scratch/stefan/7770550/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300329.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300329 none CCN(CC)C(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [39, 21, 21, 21, 37, 19, 21, 11, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 39, 39, 39, 39, 39, 37, 37, 37, 37, 37, 19, 19, 1, 1, 1, 2, 2, 2, 19, 19] 71 rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46]) total number of confs: 310 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300329 none CCN(CC)C(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 6, 6, 7, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 1, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1] 71 rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 45, 46, 25, 26, 5] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300329 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300329 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300329/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300329/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300329 Building REAL300000300330 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300330' /scratch/stefan/7770550/working/building/REAL300000300330 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300330 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300330/0 /scratch/stefan/7770550/working/building/REAL300000300330 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/468 `/scratch/stefan/7770550/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300330 none CCCCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 76, 49, 17, 9, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 201, 201, 201, 201, 201, 201, 201, 144, 144, 76, 76, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 201 rigid atoms, others: [40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47]) total number of confs: 887 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300330 none CCCCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 31, 23, 15, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 13, 17, 17, 17, 17, 17, 17, 1, 1, 32, 32, 32, 31, 31, 32, 32, 23, 23, 15, 15, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 46, 47, 24, 25, 38, 5] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300330 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300330 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300330/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300330 Building REAL300000300331 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300331' /scratch/stefan/7770550/working/building/REAL300000300331 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300331 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300331/0 /scratch/stefan/7770550/working/building/REAL300000300331 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/469 `/scratch/stefan/7770550/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC=C1[N+](=O)[O-]) `REAL300000300331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300331 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 5, 5, 10, 10, 10, 10, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 10, 10, 10, 10, 10, 1, 1, 1] 10 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300331 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 10, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300331 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300331 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300331/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300331 Building REAL300000300332 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300332' /scratch/stefan/7770550/working/building/REAL300000300332 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300332 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300332/0 /scratch/stefan/7770550/working/building/REAL300000300332 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/470 `/scratch/stefan/7770550/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(N2C=NN=N2)=C1) `REAL300000300332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300332 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(N2C=NN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 3, 1] 33 rigid atoms, others: [32, 33, 34, 36, 11, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300332 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(N2C=NN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 33, 33, 33, 33, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 33, 17] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300332 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(N2C=NN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 17, 33, 33, 33, 33, 33, 17, 5, 3, 5, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 33, 33, 33, 33, 33, 33, 17, 2, 3, 3, 1, 3] 33 rigid atoms, others: [35, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36]) total number of confs: 166 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300332 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300332/1 /scratch/stefan/7770550/working/building/REAL300000300332 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/471 `/scratch/stefan/7770550/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(N2C=NN=N2)=C1) `REAL300000300332.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300332 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(N2C=NN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 1] 23 rigid atoms, others: [32, 33, 35, 11, 14, 15, 16, 17, 18, 19, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300332 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(N2C=NN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 23, 23, 23, 23, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 23, 17] 23 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300332 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(N2C=NN=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 20, 23, 23, 23, 23, 23, 13, 5, 3, 5, 5, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 3, 23, 23, 23, 23, 23, 23, 2, 3, 3, 1, 3] 23 rigid atoms, others: [34, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 66 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300332 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300332 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300332/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300332/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300332 Building REAL300000300333 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300333' /scratch/stefan/7770550/working/building/REAL300000300333 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300333 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300333/0 /scratch/stefan/7770550/working/building/REAL300000300333 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/472 `/scratch/stefan/7770550/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12) `REAL300000300333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300333 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 28, 16, 16, 16, 16, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 16, 16, 16, 16, 16, 16, 30, 30, 30, 30, 30, 16, 16, 7, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16] 30 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300333 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 16, 16, 6, 7, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 6, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1] 30 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 41, 42, 43, 44, 21, 22, 23, 24, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300333 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300333/1 /scratch/stefan/7770550/working/building/REAL300000300333 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/473 `/scratch/stefan/7770550/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12) `REAL300000300333.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300333 none CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 37, 19, 19, 19, 19, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 39, 39, 39, 39, 39, 19, 19, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19] 39 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300333 none CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 7, 11, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1] 39 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 40, 41, 42, 43, 21, 22, 23, 24, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300333 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300333 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300333/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300333/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300333 Building REAL300000300334 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300334' /scratch/stefan/7770550/working/building/REAL300000300334 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300334 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300334/0 /scratch/stefan/7770550/working/building/REAL300000300334 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/474 `/scratch/stefan/7770550/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(OCCO2)C(C(=O)[O-])=C1) `REAL300000300334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300334 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(OCCO2)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 5, 5, 12, 12, 12, 12, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300334 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(OCCO2)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300334 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300334 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300334/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300334 Building REAL300000300335 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300335' /scratch/stefan/7770550/working/building/REAL300000300335 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300335 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300335/0 /scratch/stefan/7770550/working/building/REAL300000300335 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/475 `/scratch/stefan/7770550/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(SC(F)(F)F)C=C1) `REAL300000300335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300335 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(SC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 15, 15, 15, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1] 61 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300335 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(SC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 61, 61, 61, 61, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300335 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300335/1 /scratch/stefan/7770550/working/building/REAL300000300335 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/476 `/scratch/stefan/7770550/working/3D/476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(SC(F)(F)F)C=C1) `REAL300000300335.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300335 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(SC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 16, 15, 16, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 63 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300335 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(SC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 63, 63, 63, 63, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300335 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300335 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300335/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300335/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300335 Building REAL300000300336 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300336' /scratch/stefan/7770550/working/building/REAL300000300336 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300336 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300336/0 /scratch/stefan/7770550/working/building/REAL300000300336 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/477 `/scratch/stefan/7770550/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(Br)=C1) `REAL300000300336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300336 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300336 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300336 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300336/1 /scratch/stefan/7770550/working/building/REAL300000300336 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/478 `/scratch/stefan/7770550/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(Br)=C1) `REAL300000300336.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300336 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300336 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300336 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300336 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300336/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300336/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300336 Building REAL300000300337 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300337' /scratch/stefan/7770550/working/building/REAL300000300337 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300337 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300337/0 /scratch/stefan/7770550/working/building/REAL300000300337 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/479 `/scratch/stefan/7770550/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(NS(C)(=O)=O)C=C1) `REAL300000300337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300337 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(NS(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 17, 17, 17, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 11, 17, 17, 17, 1, 1] 61 rigid atoms, others: [32, 33, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300337 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(NS(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 53, 61, 61, 61, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 53, 61, 61, 61, 9, 9] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300337 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300337 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300337/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300337 Building REAL300000300338 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300338' /scratch/stefan/7770550/working/building/REAL300000300338 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300338 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300338/0 /scratch/stefan/7770550/working/building/REAL300000300338 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/480 `/scratch/stefan/7770550/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300338 none CCOCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 159, 89, 49, 17, 9, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 201, 201, 201, 201, 201, 159, 159, 89, 89, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 201 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45]) total number of confs: 735 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300338 none CCOCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 74, 32, 13, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 13, 17, 17, 17, 17, 17, 17, 1, 1, 76, 76, 76, 76, 76, 32, 32, 13, 13, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 44, 45, 24, 25] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 261 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300338 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300338 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300338/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300338 Building REAL300000300339 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300339' /scratch/stefan/7770550/working/building/REAL300000300339 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300339 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300339/0 /scratch/stefan/7770550/working/building/REAL300000300339 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/481 `/scratch/stefan/7770550/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(S(C)(=O)=O)=CC=C1F) `REAL300000300339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300339 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(S(C)(=O)=O)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 15, 15, 23, 23, 23, 23, 15, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 3, 3, 3, 1, 1] 25 rigid atoms, others: [35, 36, 11, 14, 15, 16, 17, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300339 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(S(C)(=O)=O)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 23, 23, 23, 25, 25, 25, 16, 23, 23, 23, 2, 2, 2, 1, 1, 1, 23, 25, 25, 25, 21, 23] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300339 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300339 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300339/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300339 Building REAL300000300340 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300340' /scratch/stefan/7770550/working/building/REAL300000300340 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300340 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300340/0 /scratch/stefan/7770550/working/building/REAL300000300340 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/482 `/scratch/stefan/7770550/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1[N+](=O)[O-]) `REAL300000300340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300340 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 9, 11, 11, 11, 11, 7, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 1, 1, 1] 11 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300340 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300340 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300340 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300340/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300340 Building REAL300000300341 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300341' /scratch/stefan/7770550/working/building/REAL300000300341 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300341 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300341/0 /scratch/stefan/7770550/working/building/REAL300000300341 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/483 `/scratch/stefan/7770550/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300341 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 34, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 34, 34, 34, 34, 34, 68, 1, 1, 1, 2, 2, 2, 34] 68 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300341 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 13, 34, 34, 13, 23, 34, 34, 34, 34, 34, 1, 2, 2, 2, 1, 2, 34, 34, 34, 34, 34, 34, 1] 68 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 36, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300341 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300341/1 /scratch/stefan/7770550/working/building/REAL300000300341 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/484 `/scratch/stefan/7770550/working/3D/484' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300341.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300341 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 58, 6, 1, 1, 1, 2, 2, 2, 29] 58 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300341 none CC1=CC(C(=O)[O-])=C(O)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 13, 29, 29, 13, 24, 29, 29, 29, 29, 29, 1, 2, 2, 2, 1, 2, 13, 29, 29, 29, 29, 29, 29, 1] 58 rigid atoms, others: [0, 1, 2, 3, 4, 37, 7, 8, 9, 10, 24, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300341 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300341 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300341/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300341/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300341 Building REAL300000300342 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300342' /scratch/stefan/7770550/working/building/REAL300000300342 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300342 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300342/0 /scratch/stefan/7770550/working/building/REAL300000300342 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/485 `/scratch/stefan/7770550/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCC(C(=O)[O-])CC2=C1) `REAL300000300342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300342 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCC(C(=O)[O-])CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 8, 14, 17, 17, 17, 17, 8, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 17, 17, 17, 17, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300342 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCC(C(=O)[O-])CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300342 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300342 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300342/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300342 Building REAL300000300343 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300343' /scratch/stefan/7770550/working/building/REAL300000300343 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300343 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300343/0 /scratch/stefan/7770550/working/building/REAL300000300343 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/486 `/scratch/stefan/7770550/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2=CC=CC=C2)N=C1) `REAL300000300343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300343 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1, 2, 2, 1, 2, 2, 1] 17 rigid atoms, others: [37, 11, 14, 15, 16, 17, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300343 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300343 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 2] 17 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 73 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300343 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300343 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300343/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300343 Building REAL300000300344 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300344' /scratch/stefan/7770550/working/building/REAL300000300344 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300344 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300344/0 /scratch/stefan/7770550/working/building/REAL300000300344 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/487 `/scratch/stefan/7770550/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC2=CC=CC=C2)N=C1) `REAL300000300344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300344 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 9, 17, 23, 23, 23, 23, 9, 3, 1, 3, 3, 1, 1, 1, 1, 9, 19, 19, 11, 19, 19, 1, 1, 23, 23, 23, 23, 23, 23, 1, 9, 9, 19, 19, 19, 19, 19, 1] 157 rigid atoms, others: [32, 40, 11, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300344 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 139, 157, 157, 157, 157, 157, 23, 23, 2, 2, 2, 1, 1, 1, 23, 139, 139, 157, 157, 157, 157, 157, 23] 157 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 512 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300344 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 93, 157, 157, 157, 157, 157, 93, 36, 19, 36, 36, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 19, 157, 157, 157, 157, 157, 157, 19, 4, 4, 1, 1, 1, 1, 1, 19] 157 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 665 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300344 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300344 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300344/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300344 Building REAL300000300345 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300345' /scratch/stefan/7770550/working/building/REAL300000300345 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300345 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300345/0 /scratch/stefan/7770550/working/building/REAL300000300345 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/488 `/scratch/stefan/7770550/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC2=CC=CC=C2)C=C1) `REAL300000300345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300345 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 17, 26, 26, 17, 26, 26, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 17, 17, 26, 26, 17, 26, 26, 1, 1] 62 rigid atoms, others: [35, 36, 11, 44, 45, 14, 15, 16, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300345 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 27, 62, 62, 62, 62, 62, 62, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 62, 62, 62, 62, 62, 62, 62, 15, 15] 62 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 32, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 218 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300345 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 46, 62, 62, 62, 62, 62, 46, 26, 14, 26, 26, 14, 26, 26, 14, 4, 1, 1, 1, 1, 1, 1, 1, 26, 26, 62, 62, 62, 62, 62, 62, 46, 26, 26, 4, 4, 1, 1, 1, 1, 1, 26, 26] 62 rigid atoms, others: [39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 324 number of broken/clashed sets: 24 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300345 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300345 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300345/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300345 Building REAL300000300346 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300346' /scratch/stefan/7770550/working/building/REAL300000300346 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300346 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300346/0 /scratch/stefan/7770550/working/building/REAL300000300346 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/489 `/scratch/stefan/7770550/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(F)=C1) `REAL300000300346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300346 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300346 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300346 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300346/1 /scratch/stefan/7770550/working/building/REAL300000300346 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/490 `/scratch/stefan/7770550/working/3D/490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(F)=C1) `REAL300000300346.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300346 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300346 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300346 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300346 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300346/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300346/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300346 Building REAL300000300347 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300347' /scratch/stefan/7770550/working/building/REAL300000300347 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300347 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300347/0 /scratch/stefan/7770550/working/building/REAL300000300347 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/491 `/scratch/stefan/7770550/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C(Cl)=C1) `REAL300000300347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300347 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 7, 27, 33, 33, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 27, 27, 1] 49 rigid atoms, others: [33, 34, 37, 11, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300347 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 9, 29, 49, 49, 49, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 49, 49, 9] 49 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300347 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300347 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300347/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300347 Building REAL300000300348 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300348' /scratch/stefan/7770550/working/building/REAL300000300348 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300348 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300348/0 /scratch/stefan/7770550/working/building/REAL300000300348 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/492 `/scratch/stefan/7770550/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Br)=CC=C1F) `REAL300000300348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300348 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Br)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 13, 22, 27, 27, 27, 27, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300348 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Br)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 19, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 11, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300348 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300348 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300348/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300348 Building REAL300000300349 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300349' /scratch/stefan/7770550/working/building/REAL300000300349 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300349 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300349/0 /scratch/stefan/7770550/working/building/REAL300000300349 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/493 `/scratch/stefan/7770550/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(F)(F)F) `REAL300000300349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300349 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300349 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 12, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300349 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300349 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300349/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300349 Building REAL300000300350 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300350' /scratch/stefan/7770550/working/building/REAL300000300350 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300350 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300350/0 /scratch/stefan/7770550/working/building/REAL300000300350 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/494 `/scratch/stefan/7770550/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)N(C)C(=O)N2C) `REAL300000300350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300350 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)N(C)C(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300350 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)N(C)C(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300350 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300350/1 /scratch/stefan/7770550/working/building/REAL300000300350 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/495 `/scratch/stefan/7770550/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)N(C)C(=O)N2C) `REAL300000300350.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300350 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)N(C)C(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300350 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)N(C)C(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300350 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300350 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300350/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300350/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300350 Building REAL300000300351 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300351' /scratch/stefan/7770550/working/building/REAL300000300351 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300351 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300351/0 /scratch/stefan/7770550/working/building/REAL300000300351 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/496 `/scratch/stefan/7770550/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300351 none COC(=O)C1=CSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 49, 61, 49, 49, 49, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 49, 61, 61, 61, 49, 1, 1, 1, 2, 2, 2, 49] 61 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300351 none COC(=O)C1=CSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 6, 6, 6, 25, 49, 49, 25, 25, 49, 49, 49, 49, 49, 1, 9, 9, 9, 1, 49, 49, 49, 49, 49, 49, 1] 61 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 22, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300351 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300351 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300351/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300351 Building REAL300000300352 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300352' /scratch/stefan/7770550/working/building/REAL300000300352 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300352 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300352/0 /scratch/stefan/7770550/working/building/REAL300000300352 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/497 `/scratch/stefan/7770550/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300352 none CCC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 7, 1, 1, 1, 2, 2, 2] 31 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300352 none CCC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 5, 13, 31, 31, 13, 23, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 1, 1, 1, 13, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 30, 31] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300352 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300352/1 /scratch/stefan/7770550/working/building/REAL300000300352 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/498 `/scratch/stefan/7770550/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300352.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300352 none CCC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2] 33 rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300352 none CCC1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 19, 33, 33, 19, 19, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 1, 1, 1, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 9, 10, 11, 30, 31] set([0, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300352 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300352 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300352/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300352/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300352 Building REAL300000300353 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300353' /scratch/stefan/7770550/working/building/REAL300000300353 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300353 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300353/0 /scratch/stefan/7770550/working/building/REAL300000300353 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/499 `/scratch/stefan/7770550/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=NC=CC=C21) `REAL300000300353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300353 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=NC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 11, 15, 15, 15, 15, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300353 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=NC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300353 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300353/1 /scratch/stefan/7770550/working/building/REAL300000300353 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/500 `/scratch/stefan/7770550/working/3D/500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=NC=CC=C12) `REAL300000300353.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300353 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 8, 14, 14, 14, 14, 14, 8, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300353 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 1, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300353 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300353 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300353/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300353/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300353 Building REAL300000300354 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300354' /scratch/stefan/7770550/working/building/REAL300000300354 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300354 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300354/0 /scratch/stefan/7770550/working/building/REAL300000300354 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/501 `/scratch/stefan/7770550/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC(C2=CC=C(F)C=C2)=N1) `REAL300000300354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300354 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 23, 38, 38, 38, 38, 38, 23, 6, 1, 6, 6, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 38, 38, 38, 38, 38, 38, 1, 4, 4, 4, 4] 38 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300354 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 16, 16, 16, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2, 1, 1, 1, 38, 38, 38, 38, 38] 38 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300354 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC(C2=CC=C(F)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 27, 38, 38, 38, 38, 38, 27, 13, 4, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 38, 38, 38, 38, 38, 38, 4, 1, 1, 1, 1] 38 rigid atoms, others: [33, 34, 35, 36, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 140 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300354 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300354 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300354/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300354 Building REAL300000300355 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300355' /scratch/stefan/7770550/working/building/REAL300000300355 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300355 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300355/0 /scratch/stefan/7770550/working/building/REAL300000300355 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/502 `/scratch/stefan/7770550/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1Cl) `REAL300000300355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300355 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1] 11 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300355 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300355 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300355 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300355/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300355 Building REAL300000300356 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300356' /scratch/stefan/7770550/working/building/REAL300000300356 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300356 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300356/0 /scratch/stefan/7770550/working/building/REAL300000300356 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/503 `/scratch/stefan/7770550/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C(C)=C1) `REAL300000300356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300356 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 8, 29, 37, 37, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 29, 29, 2, 2, 2, 1] 48 rigid atoms, others: [33, 34, 40, 11, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300356 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 9, 32, 48, 48, 48, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 48, 48, 9, 9, 9, 9] 48 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300356 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300356 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300356/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300356 Building REAL300000300357 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300357' /scratch/stefan/7770550/working/building/REAL300000300357 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300357 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300357/0 /scratch/stefan/7770550/working/building/REAL300000300357 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/504 `/scratch/stefan/7770550/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1) `REAL300000300357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300357 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 19, 19, 25, 25, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 68, 68, 68, 68, 68, 25, 25, 7, 1, 1, 1, 2, 2, 2, 25, 25, 25, 25] 68 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300357 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 25, 25, 11, 17, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 11, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1] 68 rigid atoms, others: [2, 3, 4, 5, 6, 7, 41, 21, 22, 23, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300357 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300357 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300357/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300357 Building REAL300000300358 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300358' /scratch/stefan/7770550/working/building/REAL300000300358 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300358 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300358/0 /scratch/stefan/7770550/working/building/REAL300000300358 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/505 `/scratch/stefan/7770550/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=NC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C12) `REAL300000300358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300358 none CC1=NN(C)C2=NC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300358 none CC1=NN(C)C2=NC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 2, 2, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 23, 24, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300358 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300358/1 /scratch/stefan/7770550/working/building/REAL300000300358 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/506 `/scratch/stefan/7770550/working/3D/506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C2=NC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C12) `REAL300000300358.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300358 none CC1=NN(C)C2=NC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300358 none CC1=NN(C)C2=NC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 38, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300358 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300358 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300358/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300358/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300358 Building REAL300000300359 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300359' /scratch/stefan/7770550/working/building/REAL300000300359 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300359 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300359/0 /scratch/stefan/7770550/working/building/REAL300000300359 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/507 `/scratch/stefan/7770550/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC2=NC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C12) `REAL300000300359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300359 none CC1=NOC2=NC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300359 none CC1=NOC2=NC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 23, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300359 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300359/1 /scratch/stefan/7770550/working/building/REAL300000300359 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/508 `/scratch/stefan/7770550/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC2=NC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C12) `REAL300000300359.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300359 none CC1=NOC2=NC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300359 none CC1=NOC2=NC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 23, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300359 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300359 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300359/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300359/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300359 Building REAL300000300360 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300360' /scratch/stefan/7770550/working/building/REAL300000300360 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300360 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300360/0 /scratch/stefan/7770550/working/building/REAL300000300360 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/509 `/scratch/stefan/7770550/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCCCl)C=C1) `REAL300000300360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300360 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCCCl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 9, 19, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 5, 5, 9, 9, 19, 19, 1, 1] 112 rigid atoms, others: [32, 39, 40, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300360 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCCCl)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 23, 55, 112, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 23, 23, 55, 55, 112, 112, 9, 9] 112 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300360 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300360 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300360/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300360 Building REAL300000300361 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300361' /scratch/stefan/7770550/working/building/REAL300000300361 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300361 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300361/0 /scratch/stefan/7770550/working/building/REAL300000300361 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/510 `/scratch/stefan/7770550/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(F)=C1F) `REAL300000300361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300361 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 17, 27, 27, 27, 27, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300361 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300361 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300361 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300361/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300361 Building REAL300000300362 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300362' /scratch/stefan/7770550/working/building/REAL300000300362 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300362 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300362/0 /scratch/stefan/7770550/working/building/REAL300000300362 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/511 `/scratch/stefan/7770550/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1) `REAL300000300362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300362 none COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 34, 44, 44, 44, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 2, 2, 2, 44] 44 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300362 none COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 28, 44, 44, 28, 35, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24, 25, 26, 27] set([32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300362 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300362 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300362/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300362 Building REAL300000300363 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300363' /scratch/stefan/7770550/working/building/REAL300000300363 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300363 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300363/0 /scratch/stefan/7770550/working/building/REAL300000300363 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/512 `/scratch/stefan/7770550/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300363 none COC(=O)C1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 29, 45, 29, 29, 23, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 45, 45, 45, 29, 29, 29, 1, 1, 1, 2, 2, 2] 45 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300363 none COC(=O)C1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 29, 29, 15, 25, 29, 29, 29, 29, 29, 5, 5, 5, 1, 1, 1, 29, 29, 29, 29, 29, 29] 45 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300363 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300363/1 /scratch/stefan/7770550/working/building/REAL300000300363 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/513 `/scratch/stefan/7770550/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300363.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300363 none COC(=O)C1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 35, 19, 19, 13, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300363 none COC(=O)C1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 9, 19, 19, 19, 19, 19, 19, 7, 7, 7, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300363 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300363 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300363/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300363/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300363 Building REAL300000300364 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300364' /scratch/stefan/7770550/working/building/REAL300000300364 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300364 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300364/0 /scratch/stefan/7770550/working/building/REAL300000300364 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/514 `/scratch/stefan/7770550/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1[N+](=O)[O-]) `REAL300000300364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300364 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 5, 5, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 1, 1, 1] 11 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300364 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300364 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300364 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300364/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300364 Building REAL300000300365 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300365' /scratch/stefan/7770550/working/building/REAL300000300365 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300365 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300365/0 /scratch/stefan/7770550/working/building/REAL300000300365 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/515 `/scratch/stefan/7770550/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C) `REAL300000300365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300365 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 11, 18, 18, 18, 18, 18, 11, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 11, 1, 1, 2, 2, 2] 18 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300365 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 18, 18] 18 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300365 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300365/1 /scratch/stefan/7770550/working/building/REAL300000300365 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/516 `/scratch/stefan/7770550/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C) `REAL300000300365.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300365 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 21, 21, 21, 21, 21, 13, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 2] 21 rigid atoms, others: [32, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300365 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300365 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300365 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300365/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300365/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300365 Building REAL300000300366 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300366' /scratch/stefan/7770550/working/building/REAL300000300366 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300366 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300366/0 /scratch/stefan/7770550/working/building/REAL300000300366 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/517 `/scratch/stefan/7770550/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCCO2) `REAL300000300366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300366 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 19, 31, 33, 33, 33, 33, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300366 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300366 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300366/1 /scratch/stefan/7770550/working/building/REAL300000300366 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/518 `/scratch/stefan/7770550/working/3D/518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCCO2) `REAL300000300366.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300366 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 20, 31, 31, 31, 31, 31, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 19, 1, 1, 1, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300366 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 7, 31, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300366 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300366 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300366/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300366/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300366 Building REAL300000300367 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300367' /scratch/stefan/7770550/working/building/REAL300000300367 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300367 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300367/0 /scratch/stefan/7770550/working/building/REAL300000300367 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/519 `/scratch/stefan/7770550/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C) `REAL300000300367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300367 none CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19] 19 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 21, 22, 23, 33, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300367 none CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 17, 19, 19, 17, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2] 19 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300367 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300367 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300367/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300367 Building REAL300000300368 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300368' /scratch/stefan/7770550/working/building/REAL300000300368 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300368 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300368/0 /scratch/stefan/7770550/working/building/REAL300000300368 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/520 `/scratch/stefan/7770550/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C(F)=C1) `REAL300000300368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300368 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 11, 29, 35, 35, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 29, 29, 1] 53 rigid atoms, others: [33, 34, 37, 11, 14, 15, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300368 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 9, 29, 53, 53, 53, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 53, 53, 9] 53 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300368 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300368 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300368/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300368 Building REAL300000300369 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300369' /scratch/stefan/7770550/working/building/REAL300000300369 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300369 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300369/0 /scratch/stefan/7770550/working/building/REAL300000300369 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/521 `/scratch/stefan/7770550/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1OC(F)F) `REAL300000300369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300369 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 7, 11, 11, 11, 11, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 9] 11 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300369 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 11, 11, 9, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300369 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300369/1 /scratch/stefan/7770550/working/building/REAL300000300369 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/522 `/scratch/stefan/7770550/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1OC(F)F) `REAL300000300369.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300369 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 19, 19, 19, 19, 19, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19, 13, 1, 1, 1, 1, 19] 24 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300369 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 19, 19, 9, 19, 19, 19, 20, 24, 24, 2, 2, 2, 1, 1, 1, 5, 19, 19, 19, 19, 24] 24 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300369 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300369 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300369/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300369/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300369 Building REAL300000300370 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300370' /scratch/stefan/7770550/working/building/REAL300000300370 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300370 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300370/0 /scratch/stefan/7770550/working/building/REAL300000300370 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/523 `/scratch/stefan/7770550/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300370 none CCOC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 101, 17, 101, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 121, 121, 121, 121, 121, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 121 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300370 none CCOC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [24, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 25, 25, 25, 24, 24, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 121 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 40, 24, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300370 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300370/1 /scratch/stefan/7770550/working/building/REAL300000300370 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/524 `/scratch/stefan/7770550/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300370.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300370 none CCOC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 113, 95, 19, 95, 19, 19, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 114, 114, 114, 114, 114, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19] 114 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300370 none CCOC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [25, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 13, 17, 19, 19, 19, 19, 19, 1, 26, 26, 26, 25, 25, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1] 114 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 39, 24, 30, 31] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300370 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300370 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300370/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300370/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300370 Building REAL300000300371 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300371' /scratch/stefan/7770550/working/building/REAL300000300371 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300371 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300371/0 /scratch/stefan/7770550/working/building/REAL300000300371 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/525 `/scratch/stefan/7770550/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300371 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 21, 21, 21, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 37, 37, 37, 37, 37, 21, 1, 1, 1, 2, 2, 2, 21] 37 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300371 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 17, 17, 21, 21, 21, 21, 21, 1, 1, 4, 4, 4, 4, 4, 1, 21, 21, 21, 21, 21, 21, 1] 37 rigid atoms, others: [1, 2, 3, 4, 5, 33, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300371 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300371 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300371/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300371 Building REAL300000300372 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300372' /scratch/stefan/7770550/working/building/REAL300000300372 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300372 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300372/0 /scratch/stefan/7770550/working/building/REAL300000300372 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/526 `/scratch/stefan/7770550/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300372 none CCCOC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 131, 96, 25, 96, 15, 25, 25, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 25, 183, 183, 183, 183, 183, 183, 183, 25, 25, 7, 1, 1, 1, 2, 2, 2, 25, 25] 183 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 643 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300372 none CCCOC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [38, 32, 16, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 9, 17, 25, 25, 25, 25, 25, 1, 1, 40, 40, 40, 39, 39, 32, 32, 1, 1, 9, 25, 25, 25, 25, 25, 25, 1, 1] 183 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 43, 24, 25, 42] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300372 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300372/1 /scratch/stefan/7770550/working/building/REAL300000300372 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/527 `/scratch/stefan/7770550/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300372.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300372 none CCCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 142, 102, 27, 102, 27, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 27, 27, 196, 196, 196, 196, 196, 196, 196, 27, 27, 1, 1, 1, 2, 2, 2, 27, 27] 196 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 622 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300372 none CCCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [42, 37, 18, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 9, 17, 27, 27, 27, 27, 27, 1, 1, 44, 43, 43, 44, 44, 36, 36, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1] 196 rigid atoms, others: [33, 34, 4, 6, 7, 8, 9, 10, 41, 24, 25, 42] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300372 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300372 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300372/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300372/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300372 Building REAL300000300373 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300373' /scratch/stefan/7770550/working/building/REAL300000300373 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300373 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300373/0 /scratch/stefan/7770550/working/building/REAL300000300373 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/528 `/scratch/stefan/7770550/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2C(=C1)C(=O)NC(=O)N2C) `REAL300000300373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300373 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2C(=C1)C(=O)NC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 27, 28, 29, 30, 31]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300373 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2C(=C1)C(=O)NC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300373 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300373/1 /scratch/stefan/7770550/working/building/REAL300000300373 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/529 `/scratch/stefan/7770550/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2C(=C1)C(=O)NC(=O)N2C) `REAL300000300373.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300373 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2C(=C1)C(=O)NC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300373 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2C(=C1)C(=O)NC(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300373 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300373 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300373/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300373/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300373 Building REAL300000300374 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300374' /scratch/stefan/7770550/working/building/REAL300000300374 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300374 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300374/0 /scratch/stefan/7770550/working/building/REAL300000300374 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/530 `/scratch/stefan/7770550/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300374 none COCC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 18, 18, 18, 18, 18, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 70, 70, 70, 70, 70, 18, 18, 18, 5, 1, 1, 1, 2, 2, 2, 18] 70 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300374 none COCC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 18, 9, 17, 18, 18, 18, 18, 18, 1, 23, 23, 23, 8, 8, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 1] 70 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 22, 38, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300374 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300374/1 /scratch/stefan/7770550/working/building/REAL300000300374 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/531 `/scratch/stefan/7770550/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300374.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300374 none COCC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 61, 61, 61, 61, 61, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 61 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300374 none COCC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 12, 17, 17, 17, 17, 17, 17, 1, 12, 12, 12, 7, 7, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1] 61 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 22, 28, 29, 30, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300374 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300374 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300374/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300374/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300374 Building REAL300000300375 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300375' /scratch/stefan/7770550/working/building/REAL300000300375 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300375 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300375/0 /scratch/stefan/7770550/working/building/REAL300000300375 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/532 `/scratch/stefan/7770550/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300375 none COC(=O)C1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 29, 45, 29, 29, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 45, 45, 45, 29, 29, 29, 1, 1, 1, 2, 2, 2] 45 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300375 none COC(=O)C1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 29, 29, 15, 15, 29, 29, 29, 29, 29, 5, 5, 5, 1, 1, 1, 29, 29, 29, 29, 29, 29] 45 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300375 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300375/1 /scratch/stefan/7770550/working/building/REAL300000300375 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/533 `/scratch/stefan/7770550/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300375.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300375 none COC(=O)C1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 35, 19, 19, 19, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300375 none COC(=O)C1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 9, 19, 19, 19, 19, 19, 19, 7, 7, 7, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300375 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300375 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300375/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300375/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300375 Building REAL300000300376 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300376' /scratch/stefan/7770550/working/building/REAL300000300376 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300376 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300376/0 /scratch/stefan/7770550/working/building/REAL300000300376 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/534 `/scratch/stefan/7770550/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1[N+](=O)[O-])OCCO2) `REAL300000300376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300376 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1[N+](=O)[O-])OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 3, 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, 5, 5, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300376 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1[N+](=O)[O-])OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300376 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300376 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300376/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300376 Building REAL300000300377 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300377' /scratch/stefan/7770550/working/building/REAL300000300377 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300377 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300377/0 /scratch/stefan/7770550/working/building/REAL300000300377 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/535 `/scratch/stefan/7770550/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=CC=C1F) `REAL300000300377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300377 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 17, 17, 33, 33, 33, 33, 17, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1, 1] 33 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300377 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 33, 33, 33, 33, 33, 33, 28, 33, 33, 33, 2, 2, 2, 1, 1, 1, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300377 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300377 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300377/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300377 Building REAL300000300378 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300378' /scratch/stefan/7770550/working/building/REAL300000300378 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300378 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300378/0 /scratch/stefan/7770550/working/building/REAL300000300378 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/536 `/scratch/stefan/7770550/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1C(F)(F)F) `REAL300000300378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300378 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300378 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300378 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300378/1 /scratch/stefan/7770550/working/building/REAL300000300378 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/537 `/scratch/stefan/7770550/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C=C1C(F)(F)F) `REAL300000300378.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300378 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 5, 13, 13, 13, 13, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 1, 1, 1] 13 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300378 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300378 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300378 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300378/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300378/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300378 Building REAL300000300379 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300379' /scratch/stefan/7770550/working/building/REAL300000300379 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300379 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300379/0 /scratch/stefan/7770550/working/building/REAL300000300379 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/538 `/scratch/stefan/7770550/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)N=C2SC=CN21) `REAL300000300379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300379 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)N=C2SC=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 8, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 19, 28, 28, 28, 28, 28, 18, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1] 28 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300379 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)N=C2SC=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 8, 1, 14, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 17, 17, 17, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 1, 1, 1, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300379 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300379 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300379/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300379 Building REAL300000300380 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300380' /scratch/stefan/7770550/working/building/REAL300000300380 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300380 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300380/0 /scratch/stefan/7770550/working/building/REAL300000300380 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/539 `/scratch/stefan/7770550/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-]) `REAL300000300380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300380 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 31, 9, 9, 9, 9, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 17, 17, 49, 49, 49, 49, 49, 9, 9, 5, 1, 1, 1, 2, 2, 2, 9] 49 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300380 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 9, 9, 5, 9, 9, 9, 9, 9, 9, 1, 1, 1, 3, 3, 9, 9, 9, 9, 9, 1, 1, 5, 9, 9, 9, 9, 9, 9, 1] 49 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300380 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300380 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300380/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300380 Building REAL300000300381 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300381' /scratch/stefan/7770550/working/building/REAL300000300381 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300381 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300381/0 /scratch/stefan/7770550/working/building/REAL300000300381 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/540 `/scratch/stefan/7770550/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2COCC2=C1) `REAL300000300381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300381 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2COCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300381 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2COCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300381 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300381/1 /scratch/stefan/7770550/working/building/REAL300000300381 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/541 `/scratch/stefan/7770550/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2COCC2=C1) `REAL300000300381.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300381 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2COCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300381 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2COCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300381 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300381 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300381/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300381/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300381 Building REAL300000300382 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300382' /scratch/stefan/7770550/working/building/REAL300000300382 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300382 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300382/0 /scratch/stefan/7770550/working/building/REAL300000300382 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/542 `/scratch/stefan/7770550/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F) `REAL300000300382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300382 none CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 107, 17, 107, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 119, 119, 119, 119, 119, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 119 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300382 none CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [32, 24, 12, 1, 12, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 33, 33, 33, 32, 32, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 119 rigid atoms, others: [3, 5, 6, 7, 8, 39, 40, 22, 23, 24, 25, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300382 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300382/1 /scratch/stefan/7770550/working/building/REAL300000300382 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/543 `/scratch/stefan/7770550/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1F) `REAL300000300382.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300382 none CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 115, 19, 115, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 132, 132, 132, 132, 132, 19, 1, 1, 1, 2, 2, 2, 19, 19] 132 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300382 none CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', '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, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [40, 24, 12, 1, 12, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 17, 17, 19, 19, 19, 19, 19, 1, 1, 1, 1, 41, 41, 41, 40, 40, 1, 19, 19, 19, 19, 19, 19, 1, 1] 132 rigid atoms, others: [3, 5, 6, 7, 8, 39, 22, 23, 24, 25, 38, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300382 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300382 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300382/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300382/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300382 Building REAL300000300383 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300383' /scratch/stefan/7770550/working/building/REAL300000300383 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300383 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300383/0 /scratch/stefan/7770550/working/building/REAL300000300383 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/544 `/scratch/stefan/7770550/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1Cl) `REAL300000300383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300383 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300383 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300383 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300383/1 /scratch/stefan/7770550/working/building/REAL300000300383 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/545 `/scratch/stefan/7770550/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1Cl) `REAL300000300383.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300383 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 15, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1] 15 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300383 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300383 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300383 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300383/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300383/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300383 Building REAL300000300384 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300384' /scratch/stefan/7770550/working/building/REAL300000300384 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300384 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300384/0 /scratch/stefan/7770550/working/building/REAL300000300384 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/546 `/scratch/stefan/7770550/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=CO1) `REAL300000300384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300384 none CC1=NC(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 17, 17, 19, 19, 19, 19, 19, 1, 1, 5, 5, 6, 6, 6, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 6] 27 rigid atoms, others: [3, 4, 5, 6, 7, 8, 39, 22, 23, 38, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300384 none CC1=NC(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 8, 8, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 1, 1, 2, 2, 2, 6, 6, 15, 27, 27, 27, 27, 27, 27, 6, 6, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 40, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300384 none CC1=NC(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 11, 11, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 27, 27, 27, 27, 27, 19, 19, 5, 1, 1, 1, 2, 2, 2, 19, 19, 27] 27 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300384 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300384/1 /scratch/stefan/7770550/working/building/REAL300000300384 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/547 `/scratch/stefan/7770550/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2)=CO1) `REAL300000300384.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300384 none CC1=NC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 1, 5, 5, 5, 5, 5, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 5] 27 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 38, 29, 30, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300384 none CC1=NC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 2, 5, 7, 7, 7, 15, 27, 27, 15, 27, 27, 27, 27, 27, 27, 5, 5, 1, 1, 2, 2, 2, 5, 5, 27, 27, 27, 27, 27, 27, 5, 5, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 39, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300384 none CC1=NC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 19, 19, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 27, 27, 27, 27, 27, 19, 19, 1, 1, 1, 2, 2, 2, 19, 19, 27] 27 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 74 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300384 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300384 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300384/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300384/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300384 Building REAL300000300385 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300385' /scratch/stefan/7770550/working/building/REAL300000300385 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300385 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300385/0 /scratch/stefan/7770550/working/building/REAL300000300385 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/548 `/scratch/stefan/7770550/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(C)CC2=C1) `REAL300000300385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300385 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 2, 2, 2, 1, 1, 1] 17 rigid atoms, others: [32, 33, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300385 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300385 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300385 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300385/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300385 Building REAL300000300386 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300386' /scratch/stefan/7770550/working/building/REAL300000300386 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300386 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300386/0 /scratch/stefan/7770550/working/building/REAL300000300386 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/549 `/scratch/stefan/7770550/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=O)NC(=O)C2=C1) `REAL300000300386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300386 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=O)NC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300386 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=O)NC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300386 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300386/1 /scratch/stefan/7770550/working/building/REAL300000300386 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/550 `/scratch/stefan/7770550/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=O)NC(=O)C2=C1) `REAL300000300386.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300386 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=O)NC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300386 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=O)NC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300386 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300386 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300386/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300386/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300386 Building REAL300000300387 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300387' /scratch/stefan/7770550/working/building/REAL300000300387 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300387 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300387/0 /scratch/stefan/7770550/working/building/REAL300000300387 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/551 `/scratch/stefan/7770550/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300387 none COC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 21, 21, 21, 21, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 27, 27, 27, 21, 21, 21, 5, 1, 1, 1, 2, 2, 2, 21] 27 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300387 none COC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 3, 3, 3, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 21, 25, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300387 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300387/1 /scratch/stefan/7770550/working/building/REAL300000300387 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/552 `/scratch/stefan/7770550/working/3D/552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300387.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300387 none COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 23 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 34, 33, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300387 none COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 13, 17, 17, 17, 17, 17, 17, 1, 3, 3, 3, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 21, 25, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300387 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300387 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300387/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300387/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300387 Building REAL300000300388 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300388' /scratch/stefan/7770550/working/building/REAL300000300388 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300388 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300388/0 /scratch/stefan/7770550/working/building/REAL300000300388 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/553 `/scratch/stefan/7770550/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300388 none CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 8, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 34, 33, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300388 none CC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 19, 19, 11, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 1, 11, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300388 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300388 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300388/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300388 Building REAL300000300389 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300389' /scratch/stefan/7770550/working/building/REAL300000300389 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300389 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300389/0 /scratch/stefan/7770550/working/building/REAL300000300389 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/554 `/scratch/stefan/7770550/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300389 none CC(=O)NC1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 33, 33, 33, 33, 33, 18, 8, 18, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 33, 84, 84, 84, 84, 33, 33, 33, 1, 1, 1, 2, 2, 2] 84 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300389 none CC(=O)NC1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 33, 33, 20, 25, 33, 33, 33, 33, 33, 1, 5, 5, 5, 5, 2, 2, 2, 33, 33, 33, 33, 33, 33] 84 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300389 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300389/1 /scratch/stefan/7770550/working/building/REAL300000300389 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/555 `/scratch/stefan/7770550/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)[N-]C1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300389.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300389 none CC(=O)[N-]C1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 113, 126, 32, 32, 32, 32, 32, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 32, 126, 126, 126, 32, 32, 32, 1, 1, 1, 2, 2, 2] 126 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 242 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300389 none CC(=O)[N-]C1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [39, 10, 39, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 15, 32, 32, 15, 18, 32, 32, 32, 32, 32, 1, 39, 39, 39, 2, 2, 2, 32, 32, 32, 32, 32, 32] 126 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300389 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300389 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300389/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300389/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300389 Building REAL300000300390 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300390' /scratch/stefan/7770550/working/building/REAL300000300390 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300390 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300390/0 /scratch/stefan/7770550/working/building/REAL300000300390 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/556 `/scratch/stefan/7770550/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CC1CCCCO1) `REAL300000300390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300390 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CC1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 55, 58, 58, 58, 58, 58, 43, 24, 8, 24, 24, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 58 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 194 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300390 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CC1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 47, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 1, 7, 47, 47, 58, 58, 58, 58, 58, 58, 58, 58, 58] 58 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300390 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300390 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300390/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300390 Building REAL300000300391 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300391' /scratch/stefan/7770550/working/building/REAL300000300391 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300391 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300391/0 /scratch/stefan/7770550/working/building/REAL300000300391 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/557 `/scratch/stefan/7770550/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F) `REAL300000300391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300391 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 57, 104, 57, 57, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 57, 57, 57, 57, 57, 104, 104, 104, 57, 1, 1, 1, 2, 2, 2, 57] 104 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300391 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 25, 57, 57, 25, 31, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 12, 12, 12, 1, 57, 57, 57, 57, 57, 57, 1] 104 rigid atoms, others: [2, 4, 5, 6, 7, 25, 21, 22, 23, 24, 36, 29] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 30, 31, 32, 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 /scratch/stefan/7770550/working/building/REAL300000300391 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300391/1 /scratch/stefan/7770550/working/building/REAL300000300391 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/558 `/scratch/stefan/7770550/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F) `REAL300000300391.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300391 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 59, 105, 59, 59, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 105, 105, 105, 59, 7, 1, 1, 1, 2, 2, 2, 59] 105 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300391 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 25, 59, 59, 25, 45, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 13, 13, 13, 1, 25, 59, 59, 59, 59, 59, 59, 1] 105 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 25, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300391 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300391 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300391/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300391/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300391 Building REAL300000300392 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300392' /scratch/stefan/7770550/working/building/REAL300000300392 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300392 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300392/0 /scratch/stefan/7770550/working/building/REAL300000300392 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/559 `/scratch/stefan/7770550/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1) `REAL300000300392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300392 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19] 19 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300392 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 19, 19, 14, 14, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300392 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300392/1 /scratch/stefan/7770550/working/building/REAL300000300392 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/560 `/scratch/stefan/7770550/working/3D/560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1) `REAL300000300392.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300392 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2, 19] 19 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300392 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 19, 19, 13, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 1, 1, 11, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300392 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300392 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300392/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300392/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300392 Building REAL300000300393 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300393' /scratch/stefan/7770550/working/building/REAL300000300393 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300393 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300393/0 /scratch/stefan/7770550/working/building/REAL300000300393 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/561 `/scratch/stefan/7770550/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300393 none COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 19, 19, 21, 21, 21, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300393 none COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 9, 15, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 9, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300393 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300393/1 /scratch/stefan/7770550/working/building/REAL300000300393 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/562 `/scratch/stefan/7770550/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300393.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300393 none COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 27, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2, 27] 27 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300393 none COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 27, 27, 13, 19, 27, 27, 27, 27, 27, 1, 1, 1, 4, 4, 4, 1, 27, 27, 27, 27, 27, 27, 1] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300393 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300393 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300393/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300393/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300393 Building REAL300000300394 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300394' /scratch/stefan/7770550/working/building/REAL300000300394 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300394 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300394/0 /scratch/stefan/7770550/working/building/REAL300000300394 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/563 `/scratch/stefan/7770550/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F) `REAL300000300394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300394 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300394 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 33, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300394 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300394 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300394/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300394 Building REAL300000300395 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300395' /scratch/stefan/7770550/working/building/REAL300000300395 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300395 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300395/0 /scratch/stefan/7770550/working/building/REAL300000300395 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/564 `/scratch/stefan/7770550/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)O1) `REAL300000300395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300395 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 41, 65, 41, 41, 41, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 65, 65, 65, 41, 41, 1, 1, 1, 2, 2, 2] 65 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 33, 32, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300395 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 6, 23, 41, 41, 35, 39, 41, 41, 41, 41, 41, 1, 13, 13, 13, 1, 1, 41, 41, 41, 41, 41, 41] 65 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300395 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300395 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300395/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300395 Building REAL300000300396 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300396' /scratch/stefan/7770550/working/building/REAL300000300396 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300396 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300396/0 /scratch/stefan/7770550/working/building/REAL300000300396 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/565 `/scratch/stefan/7770550/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=CN=C21) `REAL300000300396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300396 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 23, 27, 27, 27, 27, 27, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300396 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300396 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300396/1 /scratch/stefan/7770550/working/building/REAL300000300396 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/566 `/scratch/stefan/7770550/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=CN=C21) `REAL300000300396.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300396 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 15, 17, 25, 25, 25, 25, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 15, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300396 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300396 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300396 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300396/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300396/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300396 Building REAL300000300397 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300397' /scratch/stefan/7770550/working/building/REAL300000300397 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300397 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300397/0 /scratch/stefan/7770550/working/building/REAL300000300397 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/567 `/scratch/stefan/7770550/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(C)(=O)=O)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300397 none CC1=CC(S(C)(=O)=O)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 5, 11, 11, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 22, 22, 22, 13, 13, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 22, 22, 22, 13, 13, 13, 7, 1, 1, 1, 2, 2, 2, 13] 22 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 115 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300397 none CC1=CC(S(C)(=O)=O)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 5, 11, 11, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 5, 5, 13, 13, 13, 13, 13, 1, 2, 2, 2, 1, 4, 4, 4, 2, 2, 2, 5, 13, 13, 13, 13, 13, 13, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 43, 25, 29] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300397 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300397/1 /scratch/stefan/7770550/working/building/REAL300000300397 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/568 `/scratch/stefan/7770550/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(C)(=O)=O)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300397.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300397 none CC1=CC(S(C)(=O)=O)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 5, 11, 11, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 21, 21, 21, 12, 12, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 21, 21, 21, 12, 12, 12, 1, 1, 1, 2, 2, 2, 12] 21 rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300397 none CC1=CC(S(C)(=O)=O)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 5, 11, 11, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 12, 12, 7, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 1, 3, 3, 3, 2, 2, 2, 12, 12, 12, 12, 12, 12, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11, 42, 25, 29] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300397 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300397 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300397/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300397/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300397 Building REAL300000300398 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300398' /scratch/stefan/7770550/working/building/REAL300000300398 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300398 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300398/0 /scratch/stefan/7770550/working/building/REAL300000300398 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/569 `/scratch/stefan/7770550/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])S1) `REAL300000300398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300398 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 32, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 59 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300398 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 33, 17, 18, 19, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300398 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300398/1 /scratch/stefan/7770550/working/building/REAL300000300398 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/570 `/scratch/stefan/7770550/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])S1) `REAL300000300398.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300398 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 32, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300398 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 11, 17, 17, 11, 14, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 1, 2, 2, 2, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300398 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300398 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300398/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300398/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300398 Building REAL300000300399 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300399' /scratch/stefan/7770550/working/building/REAL300000300399 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300399 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300399/0 /scratch/stefan/7770550/working/building/REAL300000300399 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/571 `/scratch/stefan/7770550/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1C) `REAL300000300399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300399 none COC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 17, 42, 17, 17, 17, 17, 17, 8, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 42, 42, 42, 17, 17, 17, 8, 1, 1, 1, 2, 2, 2, 17, 17, 17] 42 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 141 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300399 none COC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 17, 17, 5, 11, 17, 17, 17, 17, 17, 1, 1, 11, 11, 11, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 2, 2, 2] 42 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 24, 28, 29, 30] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300399 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300399/1 /scratch/stefan/7770550/working/building/REAL300000300399 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/572 `/scratch/stefan/7770550/working/3D/572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1C) `REAL300000300399.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300399 none COC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 17, 39, 17, 17, 17, 17, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 39, 39, 39, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17, 17] 39 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300399 none COC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 17, 17, 6, 6, 17, 17, 17, 17, 17, 1, 1, 9, 9, 9, 1, 1, 1, 17, 17, 17, 17, 17, 17, 2, 2, 2] 39 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 24, 28, 29, 30] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300399 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300399 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300399/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300399/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300399 Building REAL300000300400 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300400' /scratch/stefan/7770550/working/building/REAL300000300400 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300400 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300400/0 /scratch/stefan/7770550/working/building/REAL300000300400 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/573 `/scratch/stefan/7770550/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300400 none COC1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300400 none COC1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 21, 21, 9, 13, 21, 21, 21, 21, 21, 1, 3, 3, 3, 1, 1, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 34, 22, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300400 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300400/1 /scratch/stefan/7770550/working/building/REAL300000300400 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/574 `/scratch/stefan/7770550/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300400.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300400 none COC1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 7, 1, 1, 1, 2, 2, 2, 22] 22 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300400 none COC1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 22, 22, 10, 14, 22, 22, 22, 22, 22, 1, 3, 3, 3, 1, 1, 10, 22, 22, 22, 22, 22, 22, 1] 22 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300400 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300400 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300400/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300400/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300400 Building REAL300000300401 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300401' /scratch/stefan/7770550/working/building/REAL300000300401 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300401 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300401/0 /scratch/stefan/7770550/working/building/REAL300000300401 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/575 `/scratch/stefan/7770550/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C(C)=C1) `REAL300000300401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300401 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300401 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300401 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300401/1 /scratch/stefan/7770550/working/building/REAL300000300401 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/576 `/scratch/stefan/7770550/working/3D/576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN=C1Cl) `REAL300000300401.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300401 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300401 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 33, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300401 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300401 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300401/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300401/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300401 Building REAL300000300402 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300402' /scratch/stefan/7770550/working/building/REAL300000300402 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300402 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300402/0 /scratch/stefan/7770550/working/building/REAL300000300402 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/577 `/scratch/stefan/7770550/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)NN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300402 none COC(=O)C1=C(C)NN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 95, 169, 95, 95, 95, 95, 95, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 169, 169, 169, 95, 95, 95, 95, 1, 1, 1, 2, 2, 2] 169 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300402 none COC(=O)C1=C(C)NN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 37, 95, 95, 37, 56, 95, 95, 95, 95, 95, 13, 13, 13, 2, 2, 2, 1, 95, 95, 95, 95, 95, 95] 169 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300402 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300402 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300402/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300402 Building REAL300000300403 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300403' /scratch/stefan/7770550/working/building/REAL300000300403 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300403 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300403/0 /scratch/stefan/7770550/working/building/REAL300000300403 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/578 `/scratch/stefan/7770550/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1C) `REAL300000300403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300403 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 21, 8, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 1, 1, 1, 2, 2, 2, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300403 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 31, 31, 13, 19, 31, 31, 31, 31, 31, 1, 1, 1, 1, 4, 4, 4, 1, 1, 13, 31, 31, 31, 31, 31, 31, 2, 2, 2, 2, 2, 2] 31 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 161 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300403 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300403 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300403/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300403 Building REAL300000300404 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300404' /scratch/stefan/7770550/working/building/REAL300000300404 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300404 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300404/0 /scratch/stefan/7770550/working/building/REAL300000300404 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/579 `/scratch/stefan/7770550/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300404 none COC(=O)CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 49, 129, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 129, 129, 129, 49, 49, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 129 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300404 none COC(=O)CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 4, 15, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 15, 15, 15, 4, 4, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 129 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 40, 23, 24, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300404 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300404 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300404/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300404 Building REAL300000300405 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300405' /scratch/stefan/7770550/working/building/REAL300000300405 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300405 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300405/0 /scratch/stefan/7770550/working/building/REAL300000300405 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/580 `/scratch/stefan/7770550/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCOCC1) `REAL300000300405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300405 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 17, 23, 25, 25, 25, 25, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 17, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 113 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300405 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 23, 24, 25] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300405 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300405 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300405/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300405 Building REAL300000300406 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300406' /scratch/stefan/7770550/working/building/REAL300000300406 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300406 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300406/0 /scratch/stefan/7770550/working/building/REAL300000300406 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/581 `/scratch/stefan/7770550/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)N(C)C) `REAL300000300406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300406 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 45, 45, 45, 45, 33, 33, 33, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 45, 45, 45, 45, 45, 45] 45 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300406 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 14, 17, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 3, 3, 3, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 5, 5, 5, 5, 5, 5] 45 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300406 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300406 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300406/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300406 Building REAL300000300407 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300407' /scratch/stefan/7770550/working/building/REAL300000300407 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300407 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300407/0 /scratch/stefan/7770550/working/building/REAL300000300407 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/582 `/scratch/stefan/7770550/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21) `REAL300000300407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300407 none CC(=O)N1CCC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 19, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 19, 19, 19, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 19 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 65 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300407 none CC(=O)N1CCC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 15, 17, 17, 17, 17, 17, 17, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 19 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 42, 24, 25, 33, 29, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300407 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300407/1 /scratch/stefan/7770550/working/building/REAL300000300407 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/583 `/scratch/stefan/7770550/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21) `REAL300000300407.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300407 none CC(=O)N1CCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 33, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 33, 33, 33, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 33 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300407 none CC(=O)N1CCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1] 33 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 41, 24, 25, 33, 29, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40]) total number of confs: 88 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300407 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300407 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300407/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300407/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300407 Building REAL300000300408 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300408' /scratch/stefan/7770550/working/building/REAL300000300408 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300408 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300408/0 /scratch/stefan/7770550/working/building/REAL300000300408 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/584 `/scratch/stefan/7770550/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300408 none CC1=NN(C(C)C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 43, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 2, 2, 2] 43 rigid atoms, others: [37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300408 none CC1=NN(C(C)C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 10, 10, 10, 23, 43, 43, 23, 36, 43, 43, 43, 43, 43, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 43, 43, 43, 43, 43, 43] 43 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 213 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300408 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300408 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300408/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300408 Building REAL300000300409 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300409' /scratch/stefan/7770550/working/building/REAL300000300409 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300409 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300409/0 /scratch/stefan/7770550/working/building/REAL300000300409 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/585 `/scratch/stefan/7770550/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)SC=C1) `REAL300000300409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300409 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 14, 8, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 30, 30, 30, 30, 30, 30, 1, 1, 1, 2, 2, 2, 30, 30] 30 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300409 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 21, 30, 30, 21, 27, 30, 30, 30, 30, 30, 1, 1, 1, 2, 2, 2, 30, 30, 30, 30, 30, 30, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300409 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300409 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300409/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300409 Building REAL300000300410 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300410' /scratch/stefan/7770550/working/building/REAL300000300410 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300410 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300410/0 /scratch/stefan/7770550/working/building/REAL300000300410 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/586 `/scratch/stefan/7770550/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(Cl)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300410 none COC(=O)C1=CC(Cl)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 17, 44, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 44, 44, 44, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 44 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300410 none COC(=O)C1=CC(Cl)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 8, 8, 8, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 44 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 28, 29, 37] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300410 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300410/1 /scratch/stefan/7770550/working/building/REAL300000300410 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/587 `/scratch/stefan/7770550/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(Cl)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300410.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300410 none COC(=O)C1=CC(Cl)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 17, 41, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 41, 41, 41, 17, 17, 1, 1, 1, 2, 2, 2, 17] 41 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300410 none COC(=O)C1=CC(Cl)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 7, 7, 7, 1, 1, 17, 17, 17, 17, 17, 17, 1] 41 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 36, 28, 29] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300410 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300410 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300410/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300410/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300410 Building REAL300000300411 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300411' /scratch/stefan/7770550/working/building/REAL300000300411 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300411 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300411/0 /scratch/stefan/7770550/working/building/REAL300000300411 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/588 `/scratch/stefan/7770550/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1C) `REAL300000300411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300411 none CCN1N=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 59, 59, 59, 59, 59, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 86, 86, 86, 86, 86, 59, 59, 59, 1, 1, 1, 2, 2, 2, 59, 59, 59] 86 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300411 none CCN1N=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 59, 59, 25, 43, 59, 59, 59, 59, 59, 1, 1, 6, 6, 6, 5, 5, 2, 2, 2, 59, 59, 59, 59, 59, 59, 2, 2, 2] 86 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300411 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300411/1 /scratch/stefan/7770550/working/building/REAL300000300411 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/589 `/scratch/stefan/7770550/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1C) `REAL300000300411.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300411/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300411 none CCN1N=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 55, 55, 55, 55, 55, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 79, 79, 79, 79, 79, 55, 55, 55, 8, 1, 1, 1, 2, 2, 2, 55, 55, 55] 79 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 270 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300411 none CCN1N=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 55, 55, 33, 41, 55, 55, 55, 55, 55, 1, 1, 5, 5, 5, 5, 5, 2, 2, 2, 25, 55, 55, 55, 55, 55, 55, 2, 2, 2] 79 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 273 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300411 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300411 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300411/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300411/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300411 Building REAL300000300412 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300412' /scratch/stefan/7770550/working/building/REAL300000300412 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300412 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300412/0 /scratch/stefan/7770550/working/building/REAL300000300412 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/590 `/scratch/stefan/7770550/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300412 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 19, 59, 19, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 59, 59, 59, 19, 19, 5, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19] 59 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300412 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 15, 17, 19, 19, 19, 19, 19, 1, 1, 1, 9, 9, 9, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2] 59 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 28, 29, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300412 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300412/1 /scratch/stefan/7770550/working/building/REAL300000300412 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/591 `/scratch/stefan/7770550/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300412.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300412 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 63, 19, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 63, 63, 63, 21, 21, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21] 63 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300412 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 1, 10, 10, 10, 1, 1, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2] 63 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 36, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300412 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300412 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300412/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300412/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300412 Building REAL300000300413 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300413' /scratch/stefan/7770550/working/building/REAL300000300413 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300413 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300413/0 /scratch/stefan/7770550/working/building/REAL300000300413 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/592 `/scratch/stefan/7770550/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C(C)=C1) `REAL300000300413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300413 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 2, 2, 2, 1] 17 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300413 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300413 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300413/1 /scratch/stefan/7770550/working/building/REAL300000300413 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/593 `/scratch/stefan/7770550/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C)=C1) `REAL300000300413.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300413 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 15, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1] 17 rigid atoms, others: [35, 11, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300413 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300413 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300413 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300413/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300413/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300413 Building REAL300000300414 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300414' /scratch/stefan/7770550/working/building/REAL300000300414 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300414 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300414/0 /scratch/stefan/7770550/working/building/REAL300000300414 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/594 `/scratch/stefan/7770550/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCNC(=O)C2=C1) `REAL300000300414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300414 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCNC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300414 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCNC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300414 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300414/1 /scratch/stefan/7770550/working/building/REAL300000300414 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/595 `/scratch/stefan/7770550/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCNC(=O)C2=C1) `REAL300000300414.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300414 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCNC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 8, 8, 15, 15, 15, 15, 8, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300414 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCNC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300414 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300414 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300414/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300414/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300414 Building REAL300000300415 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300415' /scratch/stefan/7770550/working/building/REAL300000300415 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300415 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300415/0 /scratch/stefan/7770550/working/building/REAL300000300415 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/596 `/scratch/stefan/7770550/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CS(C)(=O)=O)C=C1) `REAL300000300415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300415 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CS(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 7, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 16, 16, 16, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 6, 6, 17, 17, 17, 1, 1] 85 rigid atoms, others: [32, 33, 39, 40, 11, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300415 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CS(C)(=O)=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 14, 5, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 41, 85, 85, 85, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 41, 41, 85, 85, 85, 9, 9] 85 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300415 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300415 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300415/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300415 Building REAL300000300416 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300416' /scratch/stefan/7770550/working/building/REAL300000300416 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300416 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300416/0 /scratch/stefan/7770550/working/building/REAL300000300416 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/597 `/scratch/stefan/7770550/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C#N)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300416 none CC1=CC=C(C#N)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300416 none CC1=CC=C(C#N)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 19, 19, 11, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 11, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300416 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300416/1 /scratch/stefan/7770550/working/building/REAL300000300416 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/598 `/scratch/stefan/7770550/working/3D/598' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C#N)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300416.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300416 none CC1=CC=C(C#N)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300416 none CC1=CC=C(C#N)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 27, 27, 17, 23, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300416 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300416 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300416/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300416/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300416 Building REAL300000300417 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300417' /scratch/stefan/7770550/working/building/REAL300000300417 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300417 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300417/0 /scratch/stefan/7770550/working/building/REAL300000300417 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/599 `/scratch/stefan/7770550/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F) `REAL300000300417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300417 none CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 39, 39, 39, 39, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 39 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300417 none CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 4, 4, 4, 4, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 39 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 29, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300417 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300417 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300417/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300417 Building REAL300000300418 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300418' /scratch/stefan/7770550/working/building/REAL300000300418 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300418 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300418/0 /scratch/stefan/7770550/working/building/REAL300000300418 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/600 `/scratch/stefan/7770550/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1F) `REAL300000300418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300418 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 15, 25, 29, 29, 29, 29, 15, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 1] 29 rigid atoms, others: [35, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300418 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300418 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300418 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300418/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300418 Building REAL300000300419 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300419' /scratch/stefan/7770550/working/building/REAL300000300419 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300419 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300419/0 /scratch/stefan/7770550/working/building/REAL300000300419 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/601 `/scratch/stefan/7770550/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C(C)(C)C) `REAL300000300419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300419 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 3, 3, 3, 3, 3, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 3 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 20 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300419 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 17 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300419 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300419 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300419/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300419 Building REAL300000300420 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300420' /scratch/stefan/7770550/working/building/REAL300000300420 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300420 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300420/0 /scratch/stefan/7770550/working/building/REAL300000300420 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/602 `/scratch/stefan/7770550/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C2OC(C)CC2=C1) `REAL300000300420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300420 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C2OC(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 2, 2, 2, 1, 1, 1] 17 rigid atoms, others: [32, 33, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300420 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C2OC(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300420 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300420 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300420/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300420 Building REAL300000300421 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300421' /scratch/stefan/7770550/working/building/REAL300000300421 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300421 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300421/0 /scratch/stefan/7770550/working/building/REAL300000300421 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/603 `/scratch/stefan/7770550/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C) `REAL300000300421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300421 none CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 35, 35, 35, 35, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 17] 35 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300421 none CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 4, 4, 4, 4, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2] 35 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 29, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300421 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300421 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300421/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300421 Building REAL300000300422 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300422' /scratch/stefan/7770550/working/building/REAL300000300422 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300422 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300422/0 /scratch/stefan/7770550/working/building/REAL300000300422 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/604 `/scratch/stefan/7770550/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21) `REAL300000300422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300422 none CC(=O)N1CCCC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300422 none CC(=O)N1CCCC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 10, 7, 45, 11, 35, 25, 36, 26, 37, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300422 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300422/1 /scratch/stefan/7770550/working/building/REAL300000300422 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/605 `/scratch/stefan/7770550/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21) `REAL300000300422.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300422 none CC(=O)N1CCCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 16, 26, 16, 16, 16, 16, 16, 16, 16, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 26, 26, 26, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 2, 2, 2, 16] 26 rigid atoms, others: [38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300422 none CC(=O)N1CCCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 9, 16, 16, 16, 16, 16, 16, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 1] 26 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 33, 8, 9, 10, 7, 44, 11, 35, 25, 36, 26, 37, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300422 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300422 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300422/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300422/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300422 Building REAL300000300423 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300423' /scratch/stefan/7770550/working/building/REAL300000300423 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300423 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300423/0 /scratch/stefan/7770550/working/building/REAL300000300423 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/606 `/scratch/stefan/7770550/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300423 none COC1=CC(F)=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 52, 52, 52, 52, 52, 52, 52, 52, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 53, 53, 53, 52, 52, 1, 1, 1, 2, 2, 2] 53 rigid atoms, others: [13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300423 none COC1=CC(F)=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 28, 52, 52, 28, 40, 52, 52, 52, 52, 52, 4, 4, 4, 1, 1, 52, 52, 52, 52, 52, 52] 53 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300423 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300423 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300423/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300423 Building REAL300000300424 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300424' /scratch/stefan/7770550/working/building/REAL300000300424 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300424 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300424/0 /scratch/stefan/7770550/working/building/REAL300000300424 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/607 `/scratch/stefan/7770550/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1C) `REAL300000300424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300424 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300424 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 13, 13, 13, 19, 19, 13, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300424 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300424 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300424/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300424 Building REAL300000300425 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300425' /scratch/stefan/7770550/working/building/REAL300000300425 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300425 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300425/0 /scratch/stefan/7770550/working/building/REAL300000300425 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/608 `/scratch/stefan/7770550/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(CC)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300425 none CCC1=CC=CC(CC)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 23, 23, 23, 20, 23, 23, 23, 26, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 23, 20, 23, 26, 26, 26, 26, 26, 6, 1, 1, 1, 2, 2, 2] 26 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300425 none CCC1=CC=CC(CC)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 8, 8, 16, 23, 23, 20, 21, 23, 23, 23, 23, 23, 4, 4, 4, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 16, 23, 23, 23, 23, 23, 23] 26 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10, 29, 30, 31] set([0, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300425 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300425 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300425/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300425 Building REAL300000300426 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300426' /scratch/stefan/7770550/working/building/REAL300000300426 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300426 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300426/0 /scratch/stefan/7770550/working/building/REAL300000300426 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/609 `/scratch/stefan/7770550/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2CCOC2=O)C=C1) `REAL300000300426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300426 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2CCOC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 5, 5, 5, 5, 1, 1] 33 rigid atoms, others: [33, 34, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300426 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2CCOC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 33, 33, 33, 33, 9, 9] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300426 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N2CCOC2=O)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 12, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 31, 33, 33, 33, 33, 33, 17, 5, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 33, 33, 33, 33, 33, 33, 17, 5, 5, 1, 1, 1, 1, 5, 5] 33 rigid atoms, others: [35, 36, 37, 38, 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, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300426 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300426 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300426/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300426 Building REAL300000300427 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300427' /scratch/stefan/7770550/working/building/REAL300000300427 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300427 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300427/0 /scratch/stefan/7770550/working/building/REAL300000300427 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/610 `/scratch/stefan/7770550/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1OC) `REAL300000300427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300427 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 21, 78, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 46, 78, 78, 78, 21, 7, 1, 1, 1, 2, 2, 2, 21, 21, 46, 46, 46] 78 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300427 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 1, 1, 3, 11, 11, 11, 1, 9, 21, 21, 21, 21, 21, 21, 1, 1, 4, 4, 4] 78 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 38, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300427 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300427 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300427/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300427 Building REAL300000300428 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300428' /scratch/stefan/7770550/working/building/REAL300000300428 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300428 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300428/0 /scratch/stefan/7770550/working/building/REAL300000300428 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/611 `/scratch/stefan/7770550/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1F) `REAL300000300428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300428 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 11, 19, 19, 19, 19, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300428 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300428 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300428 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300428/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300428 Building REAL300000300429 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300429' /scratch/stefan/7770550/working/building/REAL300000300429 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300429 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300429/0 /scratch/stefan/7770550/working/building/REAL300000300429 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/612 `/scratch/stefan/7770550/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2O1) `REAL300000300429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300429 none CC1=NC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300429 none CC1=NC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300429 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300429/1 /scratch/stefan/7770550/working/building/REAL300000300429 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/613 `/scratch/stefan/7770550/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2O1) `REAL300000300429.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300429 none CC1=NC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300429 none CC1=NC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300429 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300429 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300429/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300429/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300429 Building REAL300000300430 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300430' /scratch/stefan/7770550/working/building/REAL300000300430 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300430 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300430/0 /scratch/stefan/7770550/working/building/REAL300000300430 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/614 `/scratch/stefan/7770550/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C(C)C)N=C1) `REAL300000300430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300430 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C(C)C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 16, 17, 24, 24, 24, 24, 9, 3, 1, 3, 3, 1, 1, 1, 1, 7, 7, 1, 1, 24, 24, 24, 24, 24, 24, 1, 7, 7, 7, 7, 7, 7, 7, 1] 42 rigid atoms, others: [36, 11, 14, 15, 16, 17, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300430 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C(C)C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 14, 14, 14, 24, 24, 24, 42, 42, 24, 24, 2, 2, 2, 1, 1, 1, 24, 42, 42, 42, 42, 42, 42, 42, 24] 42 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300430 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300430 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300430/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300430 Building REAL300000300431 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300431' /scratch/stefan/7770550/working/building/REAL300000300431 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300431 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300431/0 /scratch/stefan/7770550/working/building/REAL300000300431 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/615 `/scratch/stefan/7770550/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1S(N)(=O)=O) `REAL300000300431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300431 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1S(N)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 11, 11, 23, 23, 23, 23, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 4] 25 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300431 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1S(N)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 23, 23, 23, 23, 23, 23, 25, 25, 25, 2, 2, 2, 1, 1, 1, 23, 23, 23, 23, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300431 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300431 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300431/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300431 Building REAL300000300432 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300432' /scratch/stefan/7770550/working/building/REAL300000300432 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300432 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300432/0 /scratch/stefan/7770550/working/building/REAL300000300432 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/616 `/scratch/stefan/7770550/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CN=C2C=C1) `REAL300000300432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300432 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300432 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300432 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300432 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300432/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300432 Building REAL300000300433 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300433' /scratch/stefan/7770550/working/building/REAL300000300433 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300433 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300433/0 /scratch/stefan/7770550/working/building/REAL300000300433 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/617 `/scratch/stefan/7770550/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300433 none COC(=O)CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 97, 201, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 201, 201, 201, 97, 97, 19, 1, 1, 1, 2, 2, 2, 19] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 690 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300433 none COC(=O)CN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 9, 57, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 11, 17, 19, 19, 19, 19, 19, 1, 1, 57, 57, 57, 9, 9, 1, 19, 19, 19, 19, 19, 19, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 22, 23, 36, 29] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300433 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300433 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300433/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300433 Building REAL300000300434 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300434' /scratch/stefan/7770550/working/building/REAL300000300434 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300434 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300434/0 /scratch/stefan/7770550/working/building/REAL300000300434 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/618 `/scratch/stefan/7770550/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC(C(C)C)=N1) `REAL300000300434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300434 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 24, 31, 37, 37, 37, 37, 19, 6, 1, 6, 6, 1, 1, 1, 1, 1, 11, 11, 1, 37, 37, 37, 37, 37, 37, 1, 1, 11, 11, 11, 11, 11, 11, 11] 49 rigid atoms, others: [11, 14, 15, 16, 17, 18, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300434 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 37, 37, 37, 37, 49, 49, 37, 2, 2, 2, 1, 1, 1, 37, 37, 49, 49, 49, 49, 49, 49, 49] 49 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300434 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300434 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300434/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300434 Building REAL300000300435 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300435' /scratch/stefan/7770550/working/building/REAL300000300435 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300435 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300435/0 /scratch/stefan/7770550/working/building/REAL300000300435 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/619 `/scratch/stefan/7770550/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1[N+](=O)[O-]) `REAL300000300435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300435 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 5, 7, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 1, 1, 1] 11 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300435 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300435 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300435 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300435/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300435 Building REAL300000300436 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300436' /scratch/stefan/7770550/working/building/REAL300000300436 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300436 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300436/0 /scratch/stefan/7770550/working/building/REAL300000300436 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/620 `/scratch/stefan/7770550/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=NN1C1=CC=CC=N1) `REAL300000300436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300436 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=NN1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28] 28 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300436 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=NN1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 15, 28, 28, 15, 16, 28, 28, 28, 28, 28, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 1, 2, 2, 2, 2] 28 rigid atoms, others: [0, 1, 2, 3, 35, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300436 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=NN1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 7, 7, 7, 15, 28, 28, 15, 18, 28, 28, 28, 28, 28, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 2, 1, 1, 1, 1] 28 rigid atoms, others: [36, 37, 38, 39, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 126 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300436 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300436/1 /scratch/stefan/7770550/working/building/REAL300000300436 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/621 `/scratch/stefan/7770550/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=NN1C1=CC=CC=N1) `REAL300000300436.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300436 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=NN1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 15, 8, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 8, 1, 1, 1, 2, 2, 2, 31, 31, 31, 31, 31] 31 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300436 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=NN1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 15, 31, 31, 16, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 4, 4, 4, 4, 4, 2, 2, 2, 15, 31, 31, 31, 31, 31, 31, 1, 4, 4, 4, 4] 31 rigid atoms, others: [0, 1, 2, 3, 36, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300436 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=NN1C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 9, 9, 9, 17, 31, 31, 19, 31, 31, 31, 31, 31, 31, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 31, 31, 31, 31, 31, 31, 4, 1, 1, 1, 1] 31 rigid atoms, others: [37, 38, 39, 40, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300436 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300436 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300436/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300436/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300436 Building REAL300000300437 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300437' /scratch/stefan/7770550/working/building/REAL300000300437 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300437 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300437/0 /scratch/stefan/7770550/working/building/REAL300000300437 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/622 `/scratch/stefan/7770550/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(OCCS(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300437 none COC1=CC=C(OCCS(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 187, 201, 201, 175, 68, 45, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 68, 68, 45, 45, 5, 1, 1, 1, 2, 2, 2, 201, 201] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 578 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300437 none COC1=CC=C(OCCS(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 24, 41, 101, 101, 101, 158, 201, 201, 183, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 24, 24, 41, 41, 158, 201, 201, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 23, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 801 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300437 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300437 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300437/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300437 Building REAL300000300438 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300438' /scratch/stefan/7770550/working/building/REAL300000300438 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300438 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300438/0 /scratch/stefan/7770550/working/building/REAL300000300438 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/623 `/scratch/stefan/7770550/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=C(F)C(F)=C1) `REAL300000300438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300438 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1] 9 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300438 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300438 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300438/1 /scratch/stefan/7770550/working/building/REAL300000300438 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/624 `/scratch/stefan/7770550/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(F)C(F)=C1) `REAL300000300438.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300438 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 5, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1] 9 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300438 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300438 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300438 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300438/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300438/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300438 Building REAL300000300439 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300439' /scratch/stefan/7770550/working/building/REAL300000300439 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300439 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300439/0 /scratch/stefan/7770550/working/building/REAL300000300439 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/625 `/scratch/stefan/7770550/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)C(C)C)C=C1) `REAL300000300439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300439 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 5, 9, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 16, 16, 1, 1, 13, 13, 13, 13, 13, 13, 5, 1, 1, 16, 17, 17, 16, 17, 17, 17, 1, 1] 71 rigid atoms, others: [32, 33, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300439 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 71, 71, 71, 71, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13, 71, 71, 71, 71, 71, 71, 71, 13, 13] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300439 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300439/1 /scratch/stefan/7770550/working/building/REAL300000300439 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/626 `/scratch/stefan/7770550/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)C(C)C)C=C1) `REAL300000300439.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300439/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300439 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 22, 22, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 22, 22, 22, 22, 22, 22, 22, 1, 1] 72 rigid atoms, others: [32, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300439 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 72, 72, 72, 72, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 72, 72, 72, 72, 72, 72, 72, 15, 15] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300439 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300439 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300439/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300439/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300439 Building REAL300000300440 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300440' /scratch/stefan/7770550/working/building/REAL300000300440 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300440 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300440/0 /scratch/stefan/7770550/working/building/REAL300000300440 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/627 `/scratch/stefan/7770550/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOC(C)C) `REAL300000300440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300440 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 65, 97, 153, 197, 197, 2, 2, 2, 1, 1, 1, 7, 65, 65, 97, 97, 197, 197, 197, 197, 197, 197, 197] 197 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 795 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300440 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300440 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300440/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300440 Building REAL300000300441 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300441' /scratch/stefan/7770550/working/building/REAL300000300441 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300441 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300441/0 /scratch/stefan/7770550/working/building/REAL300000300441 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/628 `/scratch/stefan/7770550/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C) `REAL300000300441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300441 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 17, 41, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 41, 41, 41, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 41 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300441 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 1, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 41 rigid atoms, others: [2, 35, 4, 5, 6, 7, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300441 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300441/1 /scratch/stefan/7770550/working/building/REAL300000300441 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/629 `/scratch/stefan/7770550/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C) `REAL300000300441.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300441 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 17, 39, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 39, 39, 39, 17, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 39 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300441 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 13, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 1, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 39 rigid atoms, others: [2, 4, 5, 6, 7, 34, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300441 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300441 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300441/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300441/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300441 Building REAL300000300442 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300442' /scratch/stefan/7770550/working/building/REAL300000300442 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300442 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300442/0 /scratch/stefan/7770550/working/building/REAL300000300442 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/630 `/scratch/stefan/7770550/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300442 none CCC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 27, 70, 70, 27, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 27, 27, 7, 1, 1, 1, 2, 2, 2, 27, 27] 70 rigid atoms, others: [39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300442 none CCC(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 9, 17, 27, 27, 27, 27, 27, 1, 1, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 1, 1, 9, 27, 27, 27, 27, 27, 27, 1, 1] 70 rigid atoms, others: [2, 36, 5, 6, 7, 8, 9, 45, 46, 23, 24, 37] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300442 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300442 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300442/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300442 Building REAL300000300443 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300443' /scratch/stefan/7770550/working/building/REAL300000300443 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300443 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300443/0 /scratch/stefan/7770550/working/building/REAL300000300443 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/631 `/scratch/stefan/7770550/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300000300443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300443 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 8, 13, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1] 13 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300443 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 11, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300443 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300443/1 /scratch/stefan/7770550/working/building/REAL300000300443 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/632 `/scratch/stefan/7770550/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300000300443.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300443 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 7, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 1] 15 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300443 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300443 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300443 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300443/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300443/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300443 Building REAL300000300444 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300444' /scratch/stefan/7770550/working/building/REAL300000300444 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300444 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300444/0 /scratch/stefan/7770550/working/building/REAL300000300444 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/633 `/scratch/stefan/7770550/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000300444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300444 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 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, 11, 17, 21, 21, 21, 21, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 21, 21, 21, 21, 21, 21, 9, 1, 1, 1] 21 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300444 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 5, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300444 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300444/1 /scratch/stefan/7770550/working/building/REAL300000300444 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/634 `/scratch/stefan/7770550/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1) `REAL300000300444.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300444 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 17, 21, 21, 21, 21, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1] 21 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300444 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300444 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300444 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300444/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300444/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300444 Building REAL300000300445 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300445' /scratch/stefan/7770550/working/building/REAL300000300445 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300445 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300445/0 /scratch/stefan/7770550/working/building/REAL300000300445 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/635 `/scratch/stefan/7770550/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C2=NN=NN2C)=C1) `REAL300000300445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300445 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C2=NN=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 13, 13, 13, 13, 13, 7, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1, 5, 5, 5, 1] 31 rigid atoms, others: [33, 34, 35, 39, 11, 14, 15, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 68 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300445 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C2=NN=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 13, 13, 13, 13, 13, 31, 31, 31, 31, 31, 13, 2, 2, 2, 1, 1, 1, 5, 13, 13, 13, 31, 31, 31, 13] 31 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 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: REAL300000300445 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C2=NN=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 17, 31, 31, 31, 31, 31, 17, 9, 5, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 31, 31, 31, 31, 31, 31, 17, 5, 5, 5, 2, 2, 2, 5] 31 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 162 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300445 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300445/1 /scratch/stefan/7770550/working/building/REAL300000300445 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/636 `/scratch/stefan/7770550/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C2=NN=NN2C)=C1) `REAL300000300445.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300445 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C2=NN=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 8, 13, 13, 13, 13, 13, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 3, 3, 3, 1] 15 rigid atoms, others: [32, 33, 34, 38, 11, 14, 15, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300445 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C2=NN=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 13, 13, 13, 13, 13, 15, 15, 15, 15, 15, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13, 15, 15, 15, 13] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300445 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C2=NN=NN2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 15, 15, 15, 15, 15, 9, 5, 3, 5, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 15, 15, 1, 3, 3, 2, 2, 2, 3] 15 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300445 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300445 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300445/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300445/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300445 Building REAL300000300446 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300446' /scratch/stefan/7770550/working/building/REAL300000300446 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300446 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300446/0 /scratch/stefan/7770550/working/building/REAL300000300446 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/637 `/scratch/stefan/7770550/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2=CC=CC=C2F)N=C1) `REAL300000300446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300446 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2=CC=CC=C2F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 17, 17, 17, 17, 17, 17, 1, 6, 6, 6, 6, 1] 40 rigid atoms, others: [32, 37, 11, 14, 15, 16, 17, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300446 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2=CC=CC=C2F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 40, 40, 40, 40, 40, 40, 17, 17, 2, 2, 2, 1, 1, 1, 17, 40, 40, 40, 40, 17] 40 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300446 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2=CC=CC=C2F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 40, 22, 8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 40, 6, 1, 1, 1, 1, 6] 40 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 74 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300446 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300446 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300446/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300446 Building REAL300000300447 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300447' /scratch/stefan/7770550/working/building/REAL300000300447 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300447 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300447/0 /scratch/stefan/7770550/working/building/REAL300000300447 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/638 `/scratch/stefan/7770550/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300447 none CC1=CC(Br)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 1, 1, 1, 2, 2, 2] 38 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300447 none CC1=CC(Br)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 38, 38, 25, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 1, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300447 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300447 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300447/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300447 Building REAL300000300448 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300448' /scratch/stefan/7770550/working/building/REAL300000300448 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300448 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300448/0 /scratch/stefan/7770550/working/building/REAL300000300448 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/639 `/scratch/stefan/7770550/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C(F)=C1) `REAL300000300448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300448 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300448 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300448 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300448/1 /scratch/stefan/7770550/working/building/REAL300000300448 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/640 `/scratch/stefan/7770550/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)C(F)=C1) `REAL300000300448.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300448 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300448 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300448 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300448 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300448/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300448/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300448 Building REAL300000300449 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300449' /scratch/stefan/7770550/working/building/REAL300000300449 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300449 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300449/0 /scratch/stefan/7770550/working/building/REAL300000300449 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/641 `/scratch/stefan/7770550/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300449 none CC(=O)N(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 54, 64, 17, 54, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 64, 64, 64, 54, 54, 54, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 64 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 203 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300449 none CC(=O)N(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 8, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 8, 8, 8, 6, 6, 6, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 64 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 40, 41, 23, 24, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300449 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300449 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300449/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300449 Building REAL300000300450 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300450' /scratch/stefan/7770550/working/building/REAL300000300450 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300450 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300450/0 /scratch/stefan/7770550/working/building/REAL300000300450 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/642 `/scratch/stefan/7770550/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(F)C(C)=C1) `REAL300000300450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300450 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(F)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 9, 9, 9, 9, 9, 6, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 6, 1, 2, 2, 2, 2, 2, 2, 1] 9 rigid atoms, others: [37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300450 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(F)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300450 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300450 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300450/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300450 Building REAL300000300451 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300451' /scratch/stefan/7770550/working/building/REAL300000300451 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300451 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300451/0 /scratch/stefan/7770550/working/building/REAL300000300451 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/643 `/scratch/stefan/7770550/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(Br)=C1) `REAL300000300451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300451 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300451 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300451 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300451 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300451/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300451 Building REAL300000300452 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300452' /scratch/stefan/7770550/working/building/REAL300000300452 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300452 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300452/0 /scratch/stefan/7770550/working/building/REAL300000300452 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/644 `/scratch/stefan/7770550/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1Cl) `REAL300000300452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300452 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 17, 23, 23, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 1, 1, 1, 2, 2, 2] 23 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300452 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 23, 23, 11, 15, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 4, 4, 1, 1, 11, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300452 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300452/1 /scratch/stefan/7770550/working/building/REAL300000300452 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/645 `/scratch/stefan/7770550/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1Cl) `REAL300000300452.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300452 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 17, 23, 23, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2] 23 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300452 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(Cl)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 23, 23, 11, 11, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 4, 4, 1, 1, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300452 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300452 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300452/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300452/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300452 Building REAL300000300453 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300453' /scratch/stefan/7770550/working/building/REAL300000300453 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300453 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300453/0 /scratch/stefan/7770550/working/building/REAL300000300453 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/646 `/scratch/stefan/7770550/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1N1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300453 none COC1=CC=CC=C1N1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 13, 13, 1, 13, 13, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 9, 17, 27, 27, 27, 27, 27, 1, 1, 16, 16, 16, 13, 12, 13, 13, 1, 27, 27, 27, 27, 27, 27, 1] 107 rigid atoms, others: [34, 7, 8, 9, 10, 11, 41, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 177 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300453 none COC1=CC=CC=C1N1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 19, 19, 19, 57, 107, 107, 57, 99, 107, 107, 107, 107, 107, 13, 13, 4, 4, 4, 1, 1, 1, 1, 13, 107, 107, 107, 107, 107, 107, 13] 107 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300453 none COC1=CC=CC=C1N1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 45, 107, 107, 27, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 107, 107, 107, 107, 107, 107, 107, 27, 1, 1, 1, 2, 2, 2, 27] 107 rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 416 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300453 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300453 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300453/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300453 Building REAL300000300454 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300454' /scratch/stefan/7770550/working/building/REAL300000300454 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300454 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300454/0 /scratch/stefan/7770550/working/building/REAL300000300454 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/647 `/scratch/stefan/7770550/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)O2) `REAL300000300454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300454 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 8, 16, 16, 16, 16, 16, 8, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 1, 1, 1] 16 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300454 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 1, 16, 16, 16] 16 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300454 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300454/1 /scratch/stefan/7770550/working/building/REAL300000300454 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/648 `/scratch/stefan/7770550/working/3D/648' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)O2) `REAL300000300454.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300454 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 11, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300454 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1Cl)NC(=O)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300454 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300454 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300454/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300454/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300454 Building REAL300000300455 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300455' /scratch/stefan/7770550/working/building/REAL300000300455 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300455 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300455/0 /scratch/stefan/7770550/working/building/REAL300000300455 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/649 `/scratch/stefan/7770550/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])S1) `REAL300000300455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300455 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 20, 25, 25, 25, 25, 25, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300455 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300455 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300455 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300455/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300455 Building REAL300000300456 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300456' /scratch/stefan/7770550/working/building/REAL300000300456 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300456 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300456/0 /scratch/stefan/7770550/working/building/REAL300000300456 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/650 `/scratch/stefan/7770550/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC(C)C)C=N1) `REAL300000300456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300456 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC(C)C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 19, 31, 34, 34, 34, 34, 19, 6, 1, 6, 6, 1, 1, 1, 1, 4, 7, 7, 1, 1, 34, 34, 34, 34, 34, 34, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 1] 71 rigid atoms, others: [39, 11, 14, 15, 16, 17, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300456 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC(C)C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 34, 34, 34, 70, 71, 71, 34, 34, 2, 2, 2, 1, 1, 1, 34, 70, 70, 71, 71, 71, 71, 71, 71, 71, 34] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300456 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300456 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300456/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300456 Building REAL300000300457 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300457' /scratch/stefan/7770550/working/building/REAL300000300457 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300457 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300457/0 /scratch/stefan/7770550/working/building/REAL300000300457 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/651 `/scratch/stefan/7770550/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1) `REAL300000300457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300457 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1] 9 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300457 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300457 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300457/1 /scratch/stefan/7770550/working/building/REAL300000300457 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/652 `/scratch/stefan/7770550/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1) `REAL300000300457.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300457 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 5, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1] 9 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300457 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300457 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300457 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300457/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300457/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300457 Building REAL300000300458 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300458' /scratch/stefan/7770550/working/building/REAL300000300458 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300458 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300458/0 /scratch/stefan/7770550/working/building/REAL300000300458 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/653 `/scratch/stefan/7770550/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F) `REAL300000300458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300458 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 15, 21, 25, 25, 25, 25, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 2] 25 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300458 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300458 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300458/1 /scratch/stefan/7770550/working/building/REAL300000300458 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/654 `/scratch/stefan/7770550/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F) `REAL300000300458.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300458 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 21, 25, 25, 25, 25, 25, 13, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 13, 1, 1, 2, 2, 2] 25 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300458 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300458 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300458 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300458/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300458/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300458 Building REAL300000300459 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300459' /scratch/stefan/7770550/working/building/REAL300000300459 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300459 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300459/0 /scratch/stefan/7770550/working/building/REAL300000300459 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/655 `/scratch/stefan/7770550/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)C(C)(C)C)C=C1) `REAL300000300459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300459 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 25 rigid atoms, others: [33, 34, 44, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 93 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300459 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 25, 25, 25, 25, 25, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 15, 15] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300459 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300459/1 /scratch/stefan/7770550/working/building/REAL300000300459 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/656 `/scratch/stefan/7770550/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)C(C)(C)C)C=C1) `REAL300000300459.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300459 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 23 rigid atoms, others: [32, 33, 43, 44, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 82 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300459 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)C(C)(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 23, 23, 23, 23, 23, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 15] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300459 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300459 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300459/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300459/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300459 Building REAL300000300460 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300460' /scratch/stefan/7770550/working/building/REAL300000300460 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300460 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300460/0 /scratch/stefan/7770550/working/building/REAL300000300460 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/657 `/scratch/stefan/7770550/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(Cl)C=C1C(=O)[O-]) `REAL300000300460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300460 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 21, 21, 21, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 37, 37, 37, 37, 37, 21, 1, 1, 1, 2, 2, 2, 21] 37 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300460 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 7, 21, 21, 7, 10, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 21, 21, 21, 21, 21, 21, 1] 37 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300460 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300460/1 /scratch/stefan/7770550/working/building/REAL300000300460 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/658 `/scratch/stefan/7770550/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(Cl)C=C1C(=O)[O-]) `REAL300000300460.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300460 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 21, 21, 21, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 37, 37, 37, 37, 37, 21, 7, 1, 1, 1, 2, 2, 2, 21] 37 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300460 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(Cl)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 7, 21, 21, 7, 11, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 7, 21, 21, 21, 21, 21, 21, 1] 37 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300460 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300460 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300460/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300460/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300460 Building REAL300000300461 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300461' /scratch/stefan/7770550/working/building/REAL300000300461 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300461 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300461/0 /scratch/stefan/7770550/working/building/REAL300000300461 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/659 `/scratch/stefan/7770550/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1) `REAL300000300461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300461 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 17, 39, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 39, 39, 39, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 39 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300461 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 12, 17, 17, 17, 17, 17, 1, 1, 5, 5, 5, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 39 rigid atoms, others: [2, 35, 4, 5, 6, 7, 34, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300461 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300461/1 /scratch/stefan/7770550/working/building/REAL300000300461 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/660 `/scratch/stefan/7770550/working/3D/660' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1) `REAL300000300461.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300461 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 37, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 37, 37, 37, 17, 1, 1, 1, 2, 2, 2, 17, 17] 37 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300461 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 4, 4, 4, 1, 17, 17, 17, 17, 17, 17, 1, 1] 37 rigid atoms, others: [33, 2, 4, 5, 6, 7, 34, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300461 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300461 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300461/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300461/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300461 Building REAL300000300462 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300462' /scratch/stefan/7770550/working/building/REAL300000300462 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300462 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300462/0 /scratch/stefan/7770550/working/building/REAL300000300462 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/661 `/scratch/stefan/7770550/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F) `REAL300000300462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300462 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 15, 21, 21, 21, 21, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1] 21 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300462 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300462 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300462/1 /scratch/stefan/7770550/working/building/REAL300000300462 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/662 `/scratch/stefan/7770550/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F) `REAL300000300462.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300462 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 12, 20, 20, 20, 20, 20, 12, 6, 1, 6, 6, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 20, 20, 20, 20, 20, 20, 12, 1, 1, 1] 20 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300462 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300462 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300462 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300462/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300462/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300462 Building REAL300000300463 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300463' /scratch/stefan/7770550/working/building/REAL300000300463 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300463 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300463/0 /scratch/stefan/7770550/working/building/REAL300000300463 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/663 `/scratch/stefan/7770550/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1) `REAL300000300463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300463 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 9, 17, 19, 19, 19, 19, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1] 19 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300463 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 5, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300463 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300463 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300463/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300463 Building REAL300000300464 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300464' /scratch/stefan/7770550/working/building/REAL300000300464 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300464 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300464/0 /scratch/stefan/7770550/working/building/REAL300000300464 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/664 `/scratch/stefan/7770550/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(F)=C1C) `REAL300000300464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300464 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 17, 17, 17, 17, 17, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 11, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300464 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300464 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300464/1 /scratch/stefan/7770550/working/building/REAL300000300464 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/665 `/scratch/stefan/7770550/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(F)=C1C) `REAL300000300464.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300464 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 17, 20, 26, 26, 26, 26, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2] 26 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300464 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300464 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300464 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300464/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300464/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300464 Building REAL300000300465 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300465' /scratch/stefan/7770550/working/building/REAL300000300465 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300465 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300465/0 /scratch/stefan/7770550/working/building/REAL300000300465 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/666 `/scratch/stefan/7770550/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Br) `REAL300000300465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300465 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300465 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 17, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300465 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300465 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300465/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300465 Building REAL300000300466 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300466' /scratch/stefan/7770550/working/building/REAL300000300466 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300466 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300466/0 /scratch/stefan/7770550/working/building/REAL300000300466 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/667 `/scratch/stefan/7770550/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C) `REAL300000300466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300466 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 19, 63, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 63, 63, 63, 19, 5, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 19] 63 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300466 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 1, 1, 1, 9, 9, 9, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2] 63 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 36, 28, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300466 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300466 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300466/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300466 Building REAL300000300467 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300467' /scratch/stefan/7770550/working/building/REAL300000300467 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300467 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300467/0 /scratch/stefan/7770550/working/building/REAL300000300467 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/668 `/scratch/stefan/7770550/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CS1) `REAL300000300467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300467 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 17, 41, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 41, 41, 41, 17, 1, 1, 1, 2, 2, 2, 17] 41 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300467 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 5, 5, 5, 1, 17, 17, 17, 17, 17, 17, 1] 41 rigid atoms, others: [33, 2, 4, 5, 6, 7, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300467 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300467/1 /scratch/stefan/7770550/working/building/REAL300000300467 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/669 `/scratch/stefan/7770550/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CS1) `REAL300000300467.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300467 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 17, 44, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 44, 44, 44, 17, 5, 1, 1, 1, 2, 2, 2, 17] 44 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300467 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 4, 4, 4, 1, 9, 17, 17, 17, 17, 17, 17, 1] 44 rigid atoms, others: [2, 4, 5, 6, 7, 34, 21, 22, 26] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300467 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300467 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300467/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300467/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300467 Building REAL300000300468 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300468' /scratch/stefan/7770550/working/building/REAL300000300468 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300468 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300468/0 /scratch/stefan/7770550/working/building/REAL300000300468 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/670 `/scratch/stefan/7770550/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F) `REAL300000300468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300468 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 17, 53, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 53, 53, 53, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 53 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300468 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 13, 13, 13, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 53 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 36, 28, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300468 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300468/1 /scratch/stefan/7770550/working/building/REAL300000300468 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/671 `/scratch/stefan/7770550/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1F) `REAL300000300468.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300468 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 21, 57, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 57, 57, 57, 21, 1, 1, 1, 2, 2, 2, 21, 21] 57 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300468 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 1, 1, 11, 11, 11, 1, 21, 21, 21, 21, 21, 21, 1, 1] 57 rigid atoms, others: [2, 35, 4, 5, 6, 7, 21, 22, 23, 24, 36, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300468 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300468 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300468/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300468/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300468 Building REAL300000300469 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300469' /scratch/stefan/7770550/working/building/REAL300000300469 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300469 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300469/0 /scratch/stefan/7770550/working/building/REAL300000300469 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/672 `/scratch/stefan/7770550/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300469 none CC1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 16, 8, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 2, 2, 2] 32 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 15, 16, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300469 none CC1=NC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 32, 32, 21, 22, 32, 32, 32, 32, 32, 1, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300469 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300469 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300469/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300469 Building REAL300000300470 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300470' /scratch/stefan/7770550/working/building/REAL300000300470 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300470 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300470/0 /scratch/stefan/7770550/working/building/REAL300000300470 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/673 `/scratch/stefan/7770550/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC#N)C=C1) `REAL300000300470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300470 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 7, 7, 1, 1] 29 rigid atoms, others: [34, 35, 11, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300470 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 29, 29, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 29, 29, 9, 9] 29 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300470 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300470 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300470/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300470 Building REAL300000300471 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300471' /scratch/stefan/7770550/working/building/REAL300000300471 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300471 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300471/0 /scratch/stefan/7770550/working/building/REAL300000300471 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/674 `/scratch/stefan/7770550/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C([N+](=O)[O-])C=C1C) `REAL300000300471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300471 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 10, 12, 13, 13, 13, 13, 10, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 10, 2, 2, 2, 1, 1, 2, 2, 2] 13 rigid atoms, others: [35, 36, 11, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300471 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 48 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300471 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300471/1 /scratch/stefan/7770550/working/building/REAL300000300471 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/675 `/scratch/stefan/7770550/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=C([N+](=O)[O-])C=C1C) `REAL300000300471.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300471 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 11, 13, 15, 15, 15, 15, 11, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 2, 2, 2] 15 rigid atoms, others: [34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 75 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300471 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 56 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300471 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300471 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300471/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300471/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300471 Building REAL300000300472 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300472' /scratch/stefan/7770550/working/building/REAL300000300472 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300472 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300472/0 /scratch/stefan/7770550/working/building/REAL300000300472 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/676 `/scratch/stefan/7770550/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1O) `REAL300000300472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300472 none CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 43, 43, 43, 43, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 34] 86 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300472 none CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 10, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 4, 4, 4, 4, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1, 2] 86 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 29, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 86 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300472 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300472/1 /scratch/stefan/7770550/working/building/REAL300000300472 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/677 `/scratch/stefan/7770550/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1[O-]) `REAL300000300472.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300472 none CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 43, 43, 43, 43, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 43 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300472 none CC(=O)NC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 4, 4, 4, 4, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 43 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 23, 24, 38, 29, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300472 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300472 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300472/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300472/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300472 Building REAL300000300473 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300473' /scratch/stefan/7770550/working/building/REAL300000300473 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300473 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300473/0 /scratch/stefan/7770550/working/building/REAL300000300473 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/678 `/scratch/stefan/7770550/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(Cl)=C1C) `REAL300000300473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300473 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(Cl)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 13, 18, 18, 18, 18, 18, 11, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 11, 1, 1, 2, 2, 2] 18 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300473 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(Cl)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 18, 18] 18 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300473 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300473/1 /scratch/stefan/7770550/working/building/REAL300000300473 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/679 `/scratch/stefan/7770550/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(Cl)=C1C) `REAL300000300473.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300473 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(Cl)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 19, 21, 21, 21, 21, 13, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 2] 21 rigid atoms, others: [32, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300473 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(Cl)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300473 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300473 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300473/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300473/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300473 Building REAL300000300474 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300474' /scratch/stefan/7770550/working/building/REAL300000300474 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300474 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300474/0 /scratch/stefan/7770550/working/building/REAL300000300474 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/680 `/scratch/stefan/7770550/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(F)(F)F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300474 none CC1=CC=C(C(F)(F)F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 2, 2, 2] 21 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300474 none CC1=CC=C(C(F)(F)F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 21, 21, 13, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 13, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300474 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300474 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300474/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300474 Building REAL300000300475 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300475' /scratch/stefan/7770550/working/building/REAL300000300475 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300475 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300475/0 /scratch/stefan/7770550/working/building/REAL300000300475 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/681 `/scratch/stefan/7770550/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300475 none CC1=C(Br)SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300475 none CC1=C(Br)SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 21, 21, 17, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300475 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300475 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300475/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300475 Building REAL300000300476 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300476' /scratch/stefan/7770550/working/building/REAL300000300476 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300476 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300476/0 /scratch/stefan/7770550/working/building/REAL300000300476 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/682 `/scratch/stefan/7770550/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300476 none CCC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 33, 33, 33, 33, 33, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 33 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300476 none CCC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 2, 2, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 27, 28, 29, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300476 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300476 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300476/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300476 Building REAL300000300477 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300477' /scratch/stefan/7770550/working/building/REAL300000300477 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300477 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300477/0 /scratch/stefan/7770550/working/building/REAL300000300477 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/683 `/scratch/stefan/7770550/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC(Cl)=CC=C2S1) `REAL300000300477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300477 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300477 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300477 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300477 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300477/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300477 Building REAL300000300478 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300478' /scratch/stefan/7770550/working/building/REAL300000300478 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300478 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300478/0 /scratch/stefan/7770550/working/building/REAL300000300478 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/684 `/scratch/stefan/7770550/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300478 none CC1=CC(F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300478 none CC1=CC(F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300478 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300478/1 /scratch/stefan/7770550/working/building/REAL300000300478 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/685 `/scratch/stefan/7770550/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300478.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300478 none CC1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300478 none CC1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 11, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300478 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300478 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300478/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300478/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300478 Building REAL300000300479 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300479' /scratch/stefan/7770550/working/building/REAL300000300479 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300479 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300479/0 /scratch/stefan/7770550/working/building/REAL300000300479 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/686 `/scratch/stefan/7770550/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1) `REAL300000300479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300479 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 5, 9, 11, 11, 11, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 12, 12, 53, 55, 70, 70, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 53, 53, 55, 55, 1, 1] 164 rigid atoms, others: [34, 35, 40, 41, 11, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 310 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300479 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 90, 90, 164, 164, 164, 164, 11, 11, 2, 2, 2, 1, 1, 1, 5, 11, 11, 164, 164, 164, 164, 11, 11] 164 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 627 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300479 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300479/1 /scratch/stefan/7770550/working/building/REAL300000300479 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/687 `/scratch/stefan/7770550/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1) `REAL300000300479.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300479 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 32, 36, 38, 38, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 32, 32, 35, 35, 1, 1] 76 rigid atoms, others: [33, 34, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300479 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 59, 59, 76, 76, 76, 76, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 76, 76, 76, 76, 9, 9] 76 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300479 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300479 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300479/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300479/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300479 Building REAL300000300480 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300480' /scratch/stefan/7770550/working/building/REAL300000300480 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300480 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300480/0 /scratch/stefan/7770550/working/building/REAL300000300480 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/688 `/scratch/stefan/7770550/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)OC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300480 none COC(=O)C1=C(C)OC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 43, 69, 43, 43, 43, 43, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 69, 69, 69, 43, 43, 43, 1, 1, 1, 2, 2, 2, 43] 69 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300480 none COC(=O)C1=C(C)OC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 43, 43, 28, 39, 43, 43, 43, 43, 43, 1, 9, 9, 9, 2, 2, 2, 43, 43, 43, 43, 43, 43, 1] 69 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 36] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300480 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300480 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300480/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300480 Building REAL300000300481 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300481' /scratch/stefan/7770550/working/building/REAL300000300481 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300481 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300481/0 /scratch/stefan/7770550/working/building/REAL300000300481 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/689 `/scratch/stefan/7770550/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)C=CC2=C1) `REAL300000300481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300481 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300481 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300481 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300481 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300481/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300481 Building REAL300000300482 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300482' /scratch/stefan/7770550/working/building/REAL300000300482 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300482 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300482/0 /scratch/stefan/7770550/working/building/REAL300000300482 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/690 `/scratch/stefan/7770550/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300000300482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300482 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1] 9 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300482 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300482 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300482/1 /scratch/stefan/7770550/working/building/REAL300000300482 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/691 `/scratch/stefan/7770550/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300000300482.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300482 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1] 9 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300482 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300482 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300482 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300482/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300482/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300482 Building REAL300000300483 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300483' /scratch/stefan/7770550/working/building/REAL300000300483 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300483 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300483/0 /scratch/stefan/7770550/working/building/REAL300000300483 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/692 `/scratch/stefan/7770550/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC2=CC=C(Cl)C=C21) `REAL300000300483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300483 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 17, 17, 33, 33, 33, 33, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300483 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300483 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300483/1 /scratch/stefan/7770550/working/building/REAL300000300483 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/693 `/scratch/stefan/7770550/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC2=CC=C(Cl)C=C21) `REAL300000300483.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300483 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 26, 33, 33, 33, 33, 33, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 17, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300483 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 7, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300483 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300483 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300483/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300483/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300483 Building REAL300000300484 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300484' /scratch/stefan/7770550/working/building/REAL300000300484 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300484 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300484/0 /scratch/stefan/7770550/working/building/REAL300000300484 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/694 `/scratch/stefan/7770550/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300484 none COC(=O)C1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 51, 112, 51, 51, 51, 51, 51, 73, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 51, 112, 112, 112, 51, 51, 73, 73, 73, 1, 1, 1, 2, 2, 2, 51] 112 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300484 none COC(=O)C1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 25, 51, 51, 25, 39, 51, 51, 51, 51, 51, 1, 12, 12, 12, 1, 1, 4, 4, 4, 51, 51, 51, 51, 51, 51, 1] 112 rigid atoms, others: [2, 4, 5, 6, 7, 8, 10, 11, 40, 25, 29, 30] set([0, 1, 3, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300484 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300484/1 /scratch/stefan/7770550/working/building/REAL300000300484 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/695 `/scratch/stefan/7770550/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300484.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300484 none COC(=O)C1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 53, 101, 53, 53, 53, 53, 53, 61, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 101, 101, 101, 53, 53, 61, 61, 61, 7, 1, 1, 1, 2, 2, 2, 53] 101 rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300484 none COC(=O)C1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [13, 13, 1, 13, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 25, 53, 53, 42, 47, 53, 53, 53, 53, 53, 1, 13, 13, 13, 1, 1, 4, 4, 4, 25, 53, 53, 53, 53, 53, 53, 1] 101 rigid atoms, others: [2, 4, 5, 6, 7, 8, 41, 10, 11, 25, 29, 30] set([0, 1, 3, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300484 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300484 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300484/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300484/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300484 Building REAL300000300485 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300485' /scratch/stefan/7770550/working/building/REAL300000300485 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300485 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300485/0 /scratch/stefan/7770550/working/building/REAL300000300485 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/696 `/scratch/stefan/7770550/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300485 none COC(=O)C1=CC(C)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 37, 17, 17, 17, 17, 17, 17, 17, 8, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 37, 37, 37, 17, 17, 17, 17, 17, 17, 17, 8, 1, 1, 1, 2, 2, 2, 17] 37 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300485 none COC(=O)C1=CC(C)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 5, 17, 17, 5, 9, 17, 17, 17, 17, 17, 1, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 5, 17, 17, 17, 17, 17, 17, 1] 37 rigid atoms, others: [2, 43, 4, 5, 6, 7, 8, 9, 10, 11, 25, 29] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300485 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300485/1 /scratch/stefan/7770550/working/building/REAL300000300485 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/697 `/scratch/stefan/7770550/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300485.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300485 none COC(=O)C1=CC(C)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 18, 36, 18, 18, 18, 18, 18, 18, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 18, 36, 36, 36, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 2, 2, 2, 18] 36 rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300485 none COC(=O)C1=CC(C)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 18, 18, 7, 7, 18, 18, 18, 18, 18, 1, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 1] 36 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 42, 25, 29] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300485 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300485 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300485/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300485/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300485 Building REAL300000300486 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300486' /scratch/stefan/7770550/working/building/REAL300000300486 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300486 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300486/0 /scratch/stefan/7770550/working/building/REAL300000300486 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/698 `/scratch/stefan/7770550/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(C)(C)CC2=C1) `REAL300000300486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300486 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(C)(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1] 17 rigid atoms, others: [32, 33, 40, 41, 42, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300486 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(C)(C)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300486 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300486 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300486/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300486 Building REAL300000300487 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300487' /scratch/stefan/7770550/working/building/REAL300000300487 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300487 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300487/0 /scratch/stefan/7770550/working/building/REAL300000300487 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/699 `/scratch/stefan/7770550/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F) `REAL300000300487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300487 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 25, 25, 19, 25, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2, 25] 25 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300487 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 19, 25, 25, 19, 19, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 2, 2, 2, 1, 25, 25, 25, 25, 25, 25, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 33, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300487 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300487/1 /scratch/stefan/7770550/working/building/REAL300000300487 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/700 `/scratch/stefan/7770550/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F) `REAL300000300487.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300487 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 19, 29, 29, 29, 29, 29, 7, 1, 1, 1, 2, 2, 2, 29] 29 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300487 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 17, 29, 29, 17, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 29, 29, 29, 29, 29, 29, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 34, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300487 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300487 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300487/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300487/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300487 Building REAL300000300488 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300488' /scratch/stefan/7770550/working/building/REAL300000300488 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300488 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300488/0 /scratch/stefan/7770550/working/building/REAL300000300488 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/701 `/scratch/stefan/7770550/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC2=CC=CC=C21) `REAL300000300488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300488 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 19, 19, 32, 32, 32, 32, 19, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1] 32 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300488 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 1, 1, 1, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300488 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300488/1 /scratch/stefan/7770550/working/building/REAL300000300488 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/702 `/scratch/stefan/7770550/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(Cl)C=CC2=CC=CC=C21) `REAL300000300488.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300488 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(Cl)C=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 18, 27, 29, 29, 29, 29, 18, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 18, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300488 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(Cl)C=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300488 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300488 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300488/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300488/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300488 Building REAL300000300489 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300489' /scratch/stefan/7770550/working/building/REAL300000300489 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300489 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300489/0 /scratch/stefan/7770550/working/building/REAL300000300489 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/703 `/scratch/stefan/7770550/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=CC=C21) `REAL300000300489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300489 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 13, 13, 13, 13, 13, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300489 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300489 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300489/1 /scratch/stefan/7770550/working/building/REAL300000300489 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/704 `/scratch/stefan/7770550/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=CC=C21) `REAL300000300489.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300489 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 9, 13, 13, 13, 13, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300489 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300489 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300489 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300489/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300489/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300489 Building REAL300000300490 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300490' /scratch/stefan/7770550/working/building/REAL300000300490 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300490 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300490/0 /scratch/stefan/7770550/working/building/REAL300000300490 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/705 `/scratch/stefan/7770550/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2C=CSC2=C1) `REAL300000300490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300490 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2C=CSC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 13, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300490 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2C=CSC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300490 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300490/1 /scratch/stefan/7770550/working/building/REAL300000300490 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/706 `/scratch/stefan/7770550/working/3D/706' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2C=CSC2=C1) `REAL300000300490.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300490 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2C=CSC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300490 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2C=CSC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300490 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300490 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300490/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300490/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300490 Building REAL300000300491 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300491' /scratch/stefan/7770550/working/building/REAL300000300491 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300491 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300491/0 /scratch/stefan/7770550/working/building/REAL300000300491 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/707 `/scratch/stefan/7770550/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1Cl) `REAL300000300491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300491 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 12, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 1] 15 rigid atoms, others: [35, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300491 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300491 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300491/1 /scratch/stefan/7770550/working/building/REAL300000300491 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/708 `/scratch/stefan/7770550/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1Cl) `REAL300000300491.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300491 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 10, 15, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 2, 2, 2, 1] 15 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300491 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300491 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300491 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300491/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300491/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300491 Building REAL300000300492 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300492' /scratch/stefan/7770550/working/building/REAL300000300492 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300492 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300492/0 /scratch/stefan/7770550/working/building/REAL300000300492 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/709 `/scratch/stefan/7770550/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(OC)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300492 none COC(=O)C1=CC(OC)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 44, 94, 44, 44, 44, 44, 59, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 94, 94, 94, 44, 59, 59, 59, 1, 1, 1, 2, 2, 2] 94 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300492 none COC(=O)C1=CC(OC)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 3, 1, 1, 11, 11, 11, 27, 44, 44, 30, 39, 44, 44, 44, 44, 44, 1, 11, 11, 11, 1, 3, 3, 3, 44, 44, 44, 44, 44, 44] 94 rigid atoms, others: [2, 4, 5, 6, 7, 9, 10, 24, 28] set([0, 1, 3, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300492 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300492 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300492/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300492 Building REAL300000300493 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300493' /scratch/stefan/7770550/working/building/REAL300000300493 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300493 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300493/0 /scratch/stefan/7770550/working/building/REAL300000300493 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/710 `/scratch/stefan/7770550/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Br)=C1C) `REAL300000300493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300493 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Br)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 11, 18, 18, 18, 18, 18, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 11, 1, 1, 1, 2, 2, 2] 18 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300493 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Br)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 14, 14, 14, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300493 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300493 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300493/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300493 Building REAL300000300494 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300494' /scratch/stefan/7770550/working/building/REAL300000300494 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300494 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300494/0 /scratch/stefan/7770550/working/building/REAL300000300494 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/711 `/scratch/stefan/7770550/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O) `REAL300000300494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300494 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 15, 21, 21, 21, 21, 21, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2] 42 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 33, 24, 25, 26, 27, 28, 29]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300494 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 42] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300494 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300494/1 /scratch/stefan/7770550/working/building/REAL300000300494 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/712 `/scratch/stefan/7770550/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1[O-]) `REAL300000300494.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300494 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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, 6, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1] 11 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300494 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300494 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300494 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300494/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300494/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300494 Building REAL300000300495 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300495' /scratch/stefan/7770550/working/building/REAL300000300495 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300495 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300495/0 /scratch/stefan/7770550/working/building/REAL300000300495 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/713 `/scratch/stefan/7770550/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1CCCC2) `REAL300000300495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300495 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 9, 9, 16, 16, 16, 16, 9, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300495 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 1, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300495 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300495 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300495/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300495 Building REAL300000300496 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300496' /scratch/stefan/7770550/working/building/REAL300000300496 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300496 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300496/0 /scratch/stefan/7770550/working/building/REAL300000300496 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/714 `/scratch/stefan/7770550/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1) `REAL300000300496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300496 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 2, 2, 1, 1] 17 rigid atoms, others: [32, 35, 36, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300496 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 17, 17, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300496 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300496 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300496/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300496 Building REAL300000300497 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300497' /scratch/stefan/7770550/working/building/REAL300000300497 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300497 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300497/0 /scratch/stefan/7770550/working/building/REAL300000300497 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/715 `/scratch/stefan/7770550/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300497 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 45, 45, 45, 45, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 45 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300497 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 4, 4, 4, 4, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 45 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 24, 38, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300497 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300497/1 /scratch/stefan/7770550/working/building/REAL300000300497 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/716 `/scratch/stefan/7770550/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300497.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300497 none CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 45, 45, 45, 45, 17, 17, 1, 1, 1, 2, 2, 2, 17] 45 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300497 none CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 4, 4, 4, 4, 1, 1, 17, 17, 17, 17, 17, 17, 1] 45 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 24, 29, 30, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300497 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300497 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300497/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300497/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300497 Building REAL300000300498 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300498' /scratch/stefan/7770550/working/building/REAL300000300498 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300498 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300498/0 /scratch/stefan/7770550/working/building/REAL300000300498 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/717 `/scratch/stefan/7770550/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)O1) `REAL300000300498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300498 none CCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 157, 137, 57, 137, 57, 57, 57, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 165, 165, 165, 165, 165, 57, 57, 1, 1, 1, 2, 2, 2] 165 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 433 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300498 none CCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [29, 18, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 6, 23, 57, 57, 36, 43, 57, 57, 57, 57, 57, 1, 28, 29, 29, 28, 28, 1, 1, 57, 57, 57, 57, 57, 57] 165 rigid atoms, others: [3, 5, 6, 7, 8, 9, 23, 29, 30] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300498 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300498 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300498/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300498 Building REAL300000300499 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300499' /scratch/stefan/7770550/working/building/REAL300000300499 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300499 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300499/0 /scratch/stefan/7770550/working/building/REAL300000300499 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/718 `/scratch/stefan/7770550/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC([N+](=O)[O-])=C1) `REAL300000300499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300499 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 12, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300499 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300499 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300499/1 /scratch/stefan/7770550/working/building/REAL300000300499 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/719 `/scratch/stefan/7770550/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC([N+](=O)[O-])=C1) `REAL300000300499.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300499 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300499 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300499 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300499 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300499/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300499/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300499 Building REAL300000300500 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300500' /scratch/stefan/7770550/working/building/REAL300000300500 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300500 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300500/0 /scratch/stefan/7770550/working/building/REAL300000300500 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/720 `/scratch/stefan/7770550/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300500 none CC(=O)C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 21, 31, 21, 21, 21, 21, 21, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 31, 31, 31, 21, 21, 1, 1, 1, 2, 2, 2, 21] 31 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300500 none CC(=O)C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 21, 21, 9, 9, 21, 21, 21, 21, 21, 1, 11, 11, 11, 1, 1, 21, 21, 21, 21, 21, 21, 1] 31 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 35, 23, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300500 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300500/1 /scratch/stefan/7770550/working/building/REAL300000300500 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/721 `/scratch/stefan/7770550/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300500.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300500 none CC(=O)C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 19, 35, 19, 19, 19, 19, 19, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 35, 35, 35, 19, 19, 7, 1, 1, 1, 2, 2, 2, 19] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300500 none CC(=O)C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 19, 19, 7, 11, 19, 19, 19, 19, 19, 1, 9, 9, 9, 1, 1, 7, 19, 19, 19, 19, 19, 19, 1] 35 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 23, 36, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300500 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300500 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300500/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300500/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300500 Building REAL300000300501 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300501' /scratch/stefan/7770550/working/building/REAL300000300501 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300501 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300501/0 /scratch/stefan/7770550/working/building/REAL300000300501 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/722 `/scratch/stefan/7770550/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)C=NN2C(C)C) `REAL300000300501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300501 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)C=NN2C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300501 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)C=NN2C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300501 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300501/1 /scratch/stefan/7770550/working/building/REAL300000300501 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/723 `/scratch/stefan/7770550/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)C=NN2C(C)C) `REAL300000300501.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300501 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)C=NN2C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300501 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)C=NN2C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300501 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300501 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300501/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300501/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300501 Building REAL300000300502 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300502' /scratch/stefan/7770550/working/building/REAL300000300502 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300502 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300502/0 /scratch/stefan/7770550/working/building/REAL300000300502 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/724 `/scratch/stefan/7770550/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(Cl)C=C1C) `REAL300000300502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300502 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300502 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 19, 13, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300502 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300502/1 /scratch/stefan/7770550/working/building/REAL300000300502 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/725 `/scratch/stefan/7770550/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(Cl)C=C1C) `REAL300000300502.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300502 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 17, 17, 25, 25, 25, 25, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 2] 25 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300502 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 25, 25, 25, 25, 25, 13, 21, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300502 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300502 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300502/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300502/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300502 Building REAL300000300503 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300503' /scratch/stefan/7770550/working/building/REAL300000300503 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300503 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300503/0 /scratch/stefan/7770550/working/building/REAL300000300503 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/726 `/scratch/stefan/7770550/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)SC=C1) `REAL300000300503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300503 none COC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 54, 54, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 54, 54, 54, 79, 79, 79, 1, 1, 1, 2, 2, 2, 54, 54] 79 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300503 none COC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 12, 12, 12, 32, 54, 54, 32, 37, 54, 54, 54, 54, 54, 1, 1, 1, 4, 4, 4, 54, 54, 54, 54, 54, 54, 1, 1] 79 rigid atoms, others: [1, 2, 3, 4, 18, 19, 20, 30, 31] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300503 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300503 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300503/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300503 Building REAL300000300504 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300504' /scratch/stefan/7770550/working/building/REAL300000300504 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300504 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300504/0 /scratch/stefan/7770550/working/building/REAL300000300504 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/727 `/scratch/stefan/7770550/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300504 none CCS(=O)(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 17, 27, 27, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 27, 27, 27, 27, 27, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 27 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300504 none CCS(=O)(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 3, 3, 3, 2, 2, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 27 rigid atoms, others: [32, 2, 5, 6, 7, 8, 9, 10, 40, 24, 30, 31] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300504 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300504/1 /scratch/stefan/7770550/working/building/REAL300000300504 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/728 `/scratch/stefan/7770550/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300504.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300504 none CCS(=O)(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 19, 27, 27, 19, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 27, 27, 27, 27, 27, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19] 27 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300504 none CCS(=O)(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 17, 17, 19, 19, 19, 19, 19, 1, 5, 5, 5, 4, 4, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1] 27 rigid atoms, others: [32, 2, 5, 6, 7, 8, 9, 10, 39, 24, 30, 31] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300504 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300504 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300504/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300504/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300504 Building REAL300000300505 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300505' /scratch/stefan/7770550/working/building/REAL300000300505 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300505 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300505/0 /scratch/stefan/7770550/working/building/REAL300000300505 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/729 `/scratch/stefan/7770550/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)OC2=CC=C(F)C=C12) `REAL300000300505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300505 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)OC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 2, 2, 2, 43, 43, 43] 43 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300505 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)OC2=CC=C(F)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 10, 10, 10, 26, 43, 43, 27, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 43, 43, 43, 43, 43, 43, 1, 1, 1] 43 rigid atoms, others: [0, 1, 2, 3, 36, 35, 34, 17, 18, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300505 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300505 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300505/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300505 Building REAL300000300506 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300506' /scratch/stefan/7770550/working/building/REAL300000300506 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300506 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300506/0 /scratch/stefan/7770550/working/building/REAL300000300506 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/730 `/scratch/stefan/7770550/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2O1) `REAL300000300506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300506 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 19, 25, 25, 25, 25, 25, 19, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300506 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 17, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300506 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300506 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300506/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300506 Building REAL300000300507 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300507' /scratch/stefan/7770550/working/building/REAL300000300507 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300507 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300507/0 /scratch/stefan/7770550/working/building/REAL300000300507 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/731 `/scratch/stefan/7770550/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2N=C(C)C=CC2=CC=C1) `REAL300000300507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300507 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2N=C(C)C=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 15, 15, 29, 29, 29, 29, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 1, 1] 29 rigid atoms, others: [34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300507 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2N=C(C)C=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300507 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300507/1 /scratch/stefan/7770550/working/building/REAL300000300507 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/732 `/scratch/stefan/7770550/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=CC=C2C=C1) `REAL300000300507.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300507 none CC1=NC2=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 1, 1, 1, 2, 2, 2, 25, 25, 25, 25, 25] 25 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300507 none CC1=NC2=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 25, 25, 21, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 39, 19, 20, 21, 22, 23, 24, 36, 38, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300507 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300507 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300507/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300507/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300507 Building REAL300000300508 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300508' /scratch/stefan/7770550/working/building/REAL300000300508 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300508 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300508/0 /scratch/stefan/7770550/working/building/REAL300000300508 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/733 `/scratch/stefan/7770550/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC(Cl)=CC=C2S1) `REAL300000300508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300508 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 26, 26, 26] 26 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300508 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 8, 8, 8, 17, 26, 26, 17, 17, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 26, 26, 26, 26, 26, 1, 1, 1] 26 rigid atoms, others: [0, 1, 2, 3, 36, 35, 34, 17, 18, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300508 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300508/1 /scratch/stefan/7770550/working/building/REAL300000300508 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/734 `/scratch/stefan/7770550/working/3D/734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC(Cl)=CC=C2S1) `REAL300000300508.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300508 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 1, 1, 1, 2, 2, 2, 27, 27, 27] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300508 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 17, 27, 27, 17, 25, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 27, 27, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 17, 18, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300508 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300508 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300508/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300508/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300508 Building REAL300000300509 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300509' /scratch/stefan/7770550/working/building/REAL300000300509 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300509 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300509/0 /scratch/stefan/7770550/working/building/REAL300000300509 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/735 `/scratch/stefan/7770550/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)C(C)(C)C2=C1) `REAL300000300509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300509 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)C(C)(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1] 17 rigid atoms, others: [33, 34, 35, 42, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300509 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)C(C)(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300509 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300509 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300509/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300509 Building REAL300000300510 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300510' /scratch/stefan/7770550/working/building/REAL300000300510 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300510 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300510/0 /scratch/stefan/7770550/working/building/REAL300000300510 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/736 `/scratch/stefan/7770550/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(Br)S1) `REAL300000300510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300510 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 69 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300510 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300510 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300510/1 /scratch/stefan/7770550/working/building/REAL300000300510 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/737 `/scratch/stefan/7770550/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(Br)S1) `REAL300000300510.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300510 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300510 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(Br)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 5, 5, 5, 11, 21, 21, 11, 11, 21, 21, 21, 21, 21, 1, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300510 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300510 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300510/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300510/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300510 Building REAL300000300511 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300511' /scratch/stefan/7770550/working/building/REAL300000300511 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300511 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300511/0 /scratch/stefan/7770550/working/building/REAL300000300511 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/738 `/scratch/stefan/7770550/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C2=CC=CC=C21) `REAL300000300511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300511 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 9, 13, 13, 13, 13, 13, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300511 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300511 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300511/1 /scratch/stefan/7770550/working/building/REAL300000300511 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/739 `/scratch/stefan/7770550/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C2=CC=CC=C21) `REAL300000300511.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300511 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 13, 13, 13, 13, 13, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300511 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300511 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300511 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300511/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300511/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300511 Building REAL300000300512 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300512' /scratch/stefan/7770550/working/building/REAL300000300512 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300512 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300512/0 /scratch/stefan/7770550/working/building/REAL300000300512 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/740 `/scratch/stefan/7770550/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC(F)=C1F) `REAL300000300512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300512 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 17, 53, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 53, 53, 53, 17, 5, 1, 1, 1, 2, 2, 2, 17] 53 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300512 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 12, 12, 12, 1, 9, 17, 17, 17, 17, 17, 17, 1] 53 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 25, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300512 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300512/1 /scratch/stefan/7770550/working/building/REAL300000300512 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/741 `/scratch/stefan/7770550/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC(F)=C1F) `REAL300000300512.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300512 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 21, 57, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 57, 57, 57, 21, 1, 1, 1, 2, 2, 2, 21] 57 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300512 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 10, 10, 10, 1, 21, 21, 21, 21, 21, 21, 1] 57 rigid atoms, others: [2, 4, 5, 6, 7, 25, 21, 22, 23, 24, 36, 29] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300512 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300512 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300512/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300512/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300512 Building REAL300000300513 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300513' /scratch/stefan/7770550/working/building/REAL300000300513 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300513 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300513/0 /scratch/stefan/7770550/working/building/REAL300000300513 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/742 `/scratch/stefan/7770550/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)SC2=CC=CC(F)=C12) `REAL300000300513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300513 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)SC2=CC=CC(F)=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 2, 2, 2, 30, 30, 30] 30 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300513 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)SC2=CC=CC(F)=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 20, 30, 30, 20, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 30, 30, 30, 30, 30, 30, 1, 1, 1] 30 rigid atoms, others: [0, 1, 2, 3, 36, 35, 34, 17, 18, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300513 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300513 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300513/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300513 Building REAL300000300514 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300514' /scratch/stefan/7770550/working/building/REAL300000300514 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300514 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300514/0 /scratch/stefan/7770550/working/building/REAL300000300514 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/743 `/scratch/stefan/7770550/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Br)=CC(C#N)=C1) `REAL300000300514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300514 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Br)=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 11, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300514 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Br)=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300514 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300514/1 /scratch/stefan/7770550/working/building/REAL300000300514 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/744 `/scratch/stefan/7770550/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Br)=CC(C#N)=C1) `REAL300000300514.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300514 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Br)=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300514 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Br)=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 17, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300514 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300514 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300514/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300514/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300514 Building REAL300000300515 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300515' /scratch/stefan/7770550/working/building/REAL300000300515 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300515 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300515/0 /scratch/stefan/7770550/working/building/REAL300000300515 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/745 `/scratch/stefan/7770550/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=CC(C)=C1F) `REAL300000300515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300515 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 17, 27, 33, 33, 33, 33, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1, 2, 2, 2] 33 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300515 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 33, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300515 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300515 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300515/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300515 Building REAL300000300516 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300516' /scratch/stefan/7770550/working/building/REAL300000300516 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300516 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300516/0 /scratch/stefan/7770550/working/building/REAL300000300516 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/746 `/scratch/stefan/7770550/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NSC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300516 none COC(=O)C1=NSC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 14, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 30, 38, 30, 30, 30, 30, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 38, 38, 38, 30, 1, 1, 1, 2, 2, 2] 38 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 32, 23, 24, 25, 26, 30, 31]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300516 none COC(=O)C1=NSC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 14, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 30, 30, 17, 17, 30, 30, 30, 30, 30, 8, 8, 8, 1, 30, 30, 30, 30, 30, 30] 38 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300516 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300516 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300516/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300516 Building REAL300000300517 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300517' /scratch/stefan/7770550/working/building/REAL300000300517 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300517 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300517/0 /scratch/stefan/7770550/working/building/REAL300000300517 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/747 `/scratch/stefan/7770550/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN2C=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=NC2=C1Cl) `REAL300000300517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300517 none CC1=NN2C=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=NC2=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300517 none CC1=NN2C=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=NC2=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 23, 24, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300517 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300517 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300517/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300517 Building REAL300000300518 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300518' /scratch/stefan/7770550/working/building/REAL300000300518 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300518 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300518/0 /scratch/stefan/7770550/working/building/REAL300000300518 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/748 `/scratch/stefan/7770550/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1Br) `REAL300000300518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300518 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 19, 19, 25, 25, 25, 25, 19, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1] 25 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300518 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 25, 25, 25, 24, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300518 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300518 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300518/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300518 Building REAL300000300519 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300519' /scratch/stefan/7770550/working/building/REAL300000300519 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300519 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300519/0 /scratch/stefan/7770550/working/building/REAL300000300519 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/749 `/scratch/stefan/7770550/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2N=C(Cl)SC2=C1) `REAL300000300519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300519 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2N=C(Cl)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 15, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300519 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2N=C(Cl)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300519 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300519/1 /scratch/stefan/7770550/working/building/REAL300000300519 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/750 `/scratch/stefan/7770550/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2N=C(Cl)SC2=C1) `REAL300000300519.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300519 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2N=C(Cl)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300519 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2N=C(Cl)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300519 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300519 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300519/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300519/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300519 Building REAL300000300520 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300520' /scratch/stefan/7770550/working/building/REAL300000300520 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300520 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300520/0 /scratch/stefan/7770550/working/building/REAL300000300520 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/751 `/scratch/stefan/7770550/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)N1C) `REAL300000300520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300520 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 19, 19, 19, 19, 19, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300520 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300520 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300520 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300520/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300520 Building REAL300000300521 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300521' /scratch/stefan/7770550/working/building/REAL300000300521 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300521 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300521/0 /scratch/stefan/7770550/working/building/REAL300000300521 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/752 `/scratch/stefan/7770550/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)C(Cl)=N1) `REAL300000300521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300521 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)C(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 13, 15, 15, 15, 15, 15, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2] 15 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300521 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)C(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300521 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300521 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300521/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300521 Building REAL300000300522 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300522' /scratch/stefan/7770550/working/building/REAL300000300522 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300522 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300522/0 /scratch/stefan/7770550/working/building/REAL300000300522 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/753 `/scratch/stefan/7770550/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300522 none COC1=CC(OC)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 17, 16, 17, 17, 23, 17, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 23, 23, 23, 15, 23, 23, 23, 17, 7, 1, 1, 1, 2, 2, 2, 17] 23 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300522 none COC1=CC(OC)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2, 2, 7, 17, 17, 7, 8, 17, 17, 17, 17, 17, 1, 3, 3, 3, 1, 3, 3, 3, 1, 7, 17, 17, 17, 17, 17, 17, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 39, 23, 27, 31] set([0, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300522 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300522/1 /scratch/stefan/7770550/working/building/REAL300000300522 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/754 `/scratch/stefan/7770550/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300522.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300522 none COC1=CC(OC)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 13, 13, 13, 13, 13, 15, 13, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 15, 15, 15, 13, 15, 15, 15, 13, 1, 1, 1, 2, 2, 2, 13] 15 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300522 none COC1=CC(OC)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2, 2, 9, 13, 13, 9, 9, 13, 13, 13, 13, 13, 1, 2, 2, 2, 1, 3, 3, 3, 1, 13, 13, 13, 13, 13, 13, 1] 15 rigid atoms, others: [1, 2, 3, 4, 5, 38, 7, 8, 9, 23, 27, 31] set([0, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300522 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300522 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300522/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300522/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300522 Building REAL300000300523 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300523' /scratch/stefan/7770550/working/building/REAL300000300523 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300523 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300523/0 /scratch/stefan/7770550/working/building/REAL300000300523 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/755 `/scratch/stefan/7770550/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C(F)C(C(=O)[O-])=C1) `REAL300000300523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300523 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 5, 11, 11, 11, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1] 11 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300523 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 5, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300523 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300523 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300523/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300523 Building REAL300000300524 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300524' /scratch/stefan/7770550/working/building/REAL300000300524 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300524 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300524/0 /scratch/stefan/7770550/working/building/REAL300000300524 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/756 `/scratch/stefan/7770550/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=NON=C21) `REAL300000300524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300524 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=NON=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 15, 15, 23, 23, 23, 23, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1] 23 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300524 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=NON=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300524 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300524 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300524/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300524 Building REAL300000300525 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300525' /scratch/stefan/7770550/working/building/REAL300000300525 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300525 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300525/0 /scratch/stefan/7770550/working/building/REAL300000300525 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/757 `/scratch/stefan/7770550/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C([N+](=O)[O-])C=CC(C)=C1C) `REAL300000300525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300525 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C([N+](=O)[O-])C=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 6, 9, 9, 9, 9, 5, 3, 1, 3, 3, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 2, 2, 2, 2] 9 rigid atoms, others: [32, 11, 14, 15, 16, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 17, 18, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 64 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300525 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C([N+](=O)[O-])C=CC(C)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 30 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300525 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300525 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300525/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300525 Building REAL300000300526 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300526' /scratch/stefan/7770550/working/building/REAL300000300526 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300526 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300526/0 /scratch/stefan/7770550/working/building/REAL300000300526 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/758 `/scratch/stefan/7770550/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)S2)=CS1) `REAL300000300526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300526 none CC1=NC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 13, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 39, 39, 25, 35, 39, 39, 39, 39, 39, 1, 12, 12, 13, 13, 13, 1, 1, 39, 39, 39, 39, 39, 39, 13] 91 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300526 none CC1=NC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 12, 37, 36, 37, 79, 91, 91, 79, 91, 91, 91, 91, 91, 91, 13, 1, 1, 2, 2, 2, 13, 13, 91, 91, 91, 91, 91, 91, 1] 91 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300526 none CC1=NC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 39, 39, 39, 39, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 91, 91, 91, 91, 91, 39, 39, 1, 1, 1, 2, 2, 2, 91] 91 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300526 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300526 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300526/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300526 Building REAL300000300527 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300527' /scratch/stefan/7770550/working/building/REAL300000300527 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300527 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300527/0 /scratch/stefan/7770550/working/building/REAL300000300527 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/759 `/scratch/stefan/7770550/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CN=C1N) `REAL300000300527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300527 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 4, 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, 15, 21, 21, 21, 21, 21, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 21 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300527 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 4, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300527 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300527/1 /scratch/stefan/7770550/working/building/REAL300000300527 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/760 `/scratch/stefan/7770550/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CN=C1N) `REAL300000300527.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300527 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 17, 17, 17, 17, 17, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 11, 1, 1, 2, 2] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300527 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300527 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300527 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300527/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300527/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300527 Building REAL300000300528 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300528' /scratch/stefan/7770550/working/building/REAL300000300528 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300528 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300528/0 /scratch/stefan/7770550/working/building/REAL300000300528 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/761 `/scratch/stefan/7770550/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300528 none CC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2] 21 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300528 none CC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 21, 21, 13, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 1, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300528 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300528 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300528/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300528 Building REAL300000300529 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300529' /scratch/stefan/7770550/working/building/REAL300000300529 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300529 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300529/0 /scratch/stefan/7770550/working/building/REAL300000300529 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/762 `/scratch/stefan/7770550/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl) `REAL300000300529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300529 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 24, 40, 24, 24, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 40, 40, 40, 24, 7, 1, 1, 1, 2, 2, 2, 24, 24] 40 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300529 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 3, 3, 3, 9, 24, 24, 9, 17, 24, 24, 24, 24, 24, 1, 1, 1, 1, 5, 5, 5, 1, 9, 24, 24, 24, 24, 24, 24, 1, 1] 40 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 36, 28, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300529 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300529/1 /scratch/stefan/7770550/working/building/REAL300000300529 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/763 `/scratch/stefan/7770550/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl) `REAL300000300529.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300529 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 25, 43, 25, 25, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 43, 43, 43, 25, 1, 1, 1, 2, 2, 2, 25, 25] 43 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300529 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 9, 17, 25, 25, 25, 25, 25, 1, 1, 1, 1, 5, 5, 5, 1, 25, 25, 25, 25, 25, 25, 1, 1] 43 rigid atoms, others: [2, 35, 4, 5, 6, 7, 21, 22, 23, 24, 36, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300529 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300529 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300529/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300529/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300529 Building REAL300000300530 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300530' /scratch/stefan/7770550/working/building/REAL300000300530 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300530 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300530/0 /scratch/stefan/7770550/working/building/REAL300000300530 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/764 `/scratch/stefan/7770550/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(F)C=C1C) `REAL300000300530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300530 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300530 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300530 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300530/1 /scratch/stefan/7770550/working/building/REAL300000300530 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/765 `/scratch/stefan/7770550/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(F)C=C1C) `REAL300000300530.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300530 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 17, 17, 25, 25, 25, 25, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 2, 2, 2] 25 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300530 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 25, 25, 25, 25, 25, 13, 21, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300530 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300530 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300530/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300530/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300530 Building REAL300000300531 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300531' /scratch/stefan/7770550/working/building/REAL300000300531 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300531 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300531/0 /scratch/stefan/7770550/working/building/REAL300000300531 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/766 `/scratch/stefan/7770550/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C) `REAL300000300531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300531 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 15, 15, 15, 15, 15, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 15, 15, 15, 15, 15, 9, 1, 1, 1, 2, 2, 2] 15 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300531 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300531 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300531 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300531/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300531 Building REAL300000300532 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300532' /scratch/stefan/7770550/working/building/REAL300000300532 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300532 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300532/0 /scratch/stefan/7770550/working/building/REAL300000300532 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/767 `/scratch/stefan/7770550/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300532 none COCCOCCS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 165, 96, 38, 30, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 200, 200, 165, 165, 38, 38, 30, 30, 5, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 807 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300532 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300532 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300532/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300532 Building REAL300000300533 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300533' /scratch/stefan/7770550/working/building/REAL300000300533 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300533 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300533/0 /scratch/stefan/7770550/working/building/REAL300000300533 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/768 `/scratch/stefan/7770550/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCS(=O)(=O)C2=C1) `REAL300000300533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300533 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCS(=O)(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 14, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300533 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCS(=O)(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 14, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300533 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300533/1 /scratch/stefan/7770550/working/building/REAL300000300533 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/769 `/scratch/stefan/7770550/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCS(=O)(=O)C2=C1) `REAL300000300533.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300533 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCS(=O)(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 14, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300533 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCS(=O)(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 14, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300533 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300533 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300533/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300533/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300533 Building REAL300000300534 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300534' /scratch/stefan/7770550/working/building/REAL300000300534 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300534 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300534/0 /scratch/stefan/7770550/working/building/REAL300000300534 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/770 `/scratch/stefan/7770550/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1) `REAL300000300534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300534 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 5, 8, 12, 12, 12, 12, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 12, 12, 12, 12, 5, 1, 2, 2, 2, 1] 12 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300534 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(F)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 5, 12, 12, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300534 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300534 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300534/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300534 Building REAL300000300535 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300535' /scratch/stefan/7770550/working/building/REAL300000300535 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300535 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300535/0 /scratch/stefan/7770550/working/building/REAL300000300535 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/771 `/scratch/stefan/7770550/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300535 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 17, 17, 17, 17, 17, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 11, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300535 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 17, 17, 11, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300535 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300535 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300535/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300535 Building REAL300000300536 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300536' /scratch/stefan/7770550/working/building/REAL300000300536 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300536 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300536/0 /scratch/stefan/7770550/working/building/REAL300000300536 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/772 `/scratch/stefan/7770550/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(F)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300536 none COC(=O)C1=C(F)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 29, 45, 29, 29, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 45, 45, 45, 29, 29, 29, 1, 1, 1, 2, 2, 2] 45 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300536 none COC(=O)C1=C(F)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 29, 29, 16, 16, 29, 29, 29, 29, 29, 5, 5, 5, 1, 1, 1, 29, 29, 29, 29, 29, 29] 45 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300536 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300536/1 /scratch/stefan/7770550/working/building/REAL300000300536 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/773 `/scratch/stefan/7770550/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(F)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300536.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300536 none COC(=O)C1=C(F)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 35, 19, 19, 19, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 35, 35, 35, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300536 none COC(=O)C1=C(F)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 9, 9, 19, 19, 19, 19, 19, 7, 7, 7, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300536 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300536 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300536/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300536/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300536 Building REAL300000300537 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300537' /scratch/stefan/7770550/working/building/REAL300000300537 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300537 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300537/0 /scratch/stefan/7770550/working/building/REAL300000300537 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/774 `/scratch/stefan/7770550/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2F)N=C1) `REAL300000300537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300537 none CC1=CN(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 3] 33 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 40, 22, 23, 24, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300537 none CC1=CN(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 2, 2, 5, 5, 5, 17, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 3, 1, 1, 2, 2, 2, 1, 3, 3, 17, 33, 33, 33, 33, 33, 33, 3, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 41, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300537 none CC1=CN(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 33, 33, 33, 33, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 33] 33 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300537 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300537 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300537/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300537 Building REAL300000300538 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300538' /scratch/stefan/7770550/working/building/REAL300000300538 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300538 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300538/0 /scratch/stefan/7770550/working/building/REAL300000300538 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/775 `/scratch/stefan/7770550/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(C)N1) `REAL300000300538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300538 none CCOC(=O)C1=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 188, 176, 48, 176, 48, 48, 48, 16, 8, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 201, 201, 201, 201, 201, 48, 48, 48, 8, 1, 1, 1, 2, 2, 2, 48, 48, 48, 48] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 533 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300538 none CCOC(=O)C1=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 17, 8, 1, 8, 1, 1, 1, 1, 1, 11, 11, 11, 24, 48, 48, 24, 38, 48, 48, 48, 48, 48, 1, 1, 1, 28, 28, 28, 27, 27, 2, 2, 2, 24, 48, 48, 48, 48, 48, 48, 2, 2, 2, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 44, 23, 24, 25] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 329 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300538 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300538/1 /scratch/stefan/7770550/working/building/REAL300000300538 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/776 `/scratch/stefan/7770550/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C)N1) `REAL300000300538.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300538 none CCOC(=O)C1=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 177, 54, 177, 54, 54, 54, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 201, 201, 201, 201, 201, 54, 54, 54, 1, 1, 1, 2, 2, 2, 54, 54, 54, 54] 201 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 535 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300538 none CCOC(=O)C1=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 20, 9, 1, 9, 1, 1, 1, 1, 1, 11, 11, 11, 24, 54, 54, 28, 38, 54, 54, 54, 54, 54, 1, 1, 1, 30, 30, 30, 29, 29, 2, 2, 2, 54, 54, 54, 54, 54, 54, 2, 2, 2, 1] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 43, 23, 24, 25] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300538 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300538 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300538/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300538/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300538 Building REAL300000300539 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300539' /scratch/stefan/7770550/working/building/REAL300000300539 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300539 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300539/0 /scratch/stefan/7770550/working/building/REAL300000300539 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/777 `/scratch/stefan/7770550/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300539 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2, 27] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300539 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 27, 27, 13, 13, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2, 1, 27, 27, 27, 27, 27, 27, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 20, 21, 22, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300539 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300539 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300539/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300539 Building REAL300000300540 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300540' /scratch/stefan/7770550/working/building/REAL300000300540 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300540 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300540/0 /scratch/stefan/7770550/working/building/REAL300000300540 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/778 `/scratch/stefan/7770550/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1[N+](=O)[O-]) `REAL300000300540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300540 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300540 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [1, 2, 3, 4, 5, 35, 19, 20, 21, 22, 36, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300540 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300540/1 /scratch/stefan/7770550/working/building/REAL300000300540 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/779 `/scratch/stefan/7770550/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1[N+](=O)[O-]) `REAL300000300540.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300540 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 2, 2, 2, 19, 19] 19 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300540 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 15, 17, 19, 19, 19, 19, 19, 1, 1, 1, 1, 2, 2, 3, 3, 3, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 36, 28, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300540 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300540 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300540/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300540/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300540 Building REAL300000300541 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300541' /scratch/stefan/7770550/working/building/REAL300000300541 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300541 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300541/0 /scratch/stefan/7770550/working/building/REAL300000300541 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/780 `/scratch/stefan/7770550/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1) `REAL300000300541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300541 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 8, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 5, 1, 2, 2, 2, 2, 2, 2, 1] 9 rigid atoms, others: [32, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300541 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300541 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300541 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300541/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300541 Building REAL300000300542 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300542' /scratch/stefan/7770550/working/building/REAL300000300542 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300542 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300542/0 /scratch/stefan/7770550/working/building/REAL300000300542 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/781 `/scratch/stefan/7770550/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=C(Cl)C=C21) `REAL300000300542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300542 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300542 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300542 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300542/1 /scratch/stefan/7770550/working/building/REAL300000300542 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/782 `/scratch/stefan/7770550/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=C(Cl)C=C21) `REAL300000300542.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300542 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300542 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=C(Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300542 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300542 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300542/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300542/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300542 Building REAL300000300543 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300543' /scratch/stefan/7770550/working/building/REAL300000300543 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300543 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300543/0 /scratch/stefan/7770550/working/building/REAL300000300543 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/783 `/scratch/stefan/7770550/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(C)(=O)=O)C(F)=C1) `REAL300000300543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300543 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(C)(=O)=O)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 3, 3, 3, 1] 33 rigid atoms, others: [32, 33, 37, 11, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300543 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(C)(=O)=O)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 33, 33, 33, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 33, 33, 33, 17] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300543 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300543/1 /scratch/stefan/7770550/working/building/REAL300000300543 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/784 `/scratch/stefan/7770550/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(C)(=O)=O)C(F)=C1) `REAL300000300543.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300543 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(C)(=O)=O)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 3, 3, 3, 1] 33 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300543 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(C)(=O)=O)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 33, 33, 33, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 33, 33, 33, 17] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300543 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300543 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300543/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300543/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300543 Building REAL300000300544 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300544' /scratch/stefan/7770550/working/building/REAL300000300544 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300544 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300544/0 /scratch/stefan/7770550/working/building/REAL300000300544 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/785 `/scratch/stefan/7770550/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1) `REAL300000300544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300544 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1] 9 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300544 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300544 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300544/1 /scratch/stefan/7770550/working/building/REAL300000300544 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/786 `/scratch/stefan/7770550/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1) `REAL300000300544.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300544 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 9, 9, 9, 9, 9, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1] 9 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300544 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300544 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300544 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300544/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300544/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300544 Building REAL300000300545 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300545' /scratch/stefan/7770550/working/building/REAL300000300545 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300545 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300545/0 /scratch/stefan/7770550/working/building/REAL300000300545 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/787 `/scratch/stefan/7770550/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC(F)=CC=C2S1) `REAL300000300545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300545 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300545 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC(F)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300545 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300545 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300545/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300545 Building REAL300000300546 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300546' /scratch/stefan/7770550/working/building/REAL300000300546 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300546 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300546/0 /scratch/stefan/7770550/working/building/REAL300000300546 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/788 `/scratch/stefan/7770550/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1CC) `REAL300000300546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300546 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 57, 39, 39, 39, 39, 39, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 57, 57, 57, 57, 57] 63 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300546 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 10, 17, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 5, 5, 5, 5, 5] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300546 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300546 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300546/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300546 Building REAL300000300547 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300547' /scratch/stefan/7770550/working/building/REAL300000300547 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300547 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300547/0 /scratch/stefan/7770550/working/building/REAL300000300547 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/789 `/scratch/stefan/7770550/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F) `REAL300000300547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300547 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 13, 22, 25, 25, 25, 25, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1] 25 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300547 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300547 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300547 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300547/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300547 Building REAL300000300548 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300548' /scratch/stefan/7770550/working/building/REAL300000300548 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300548 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300548/0 /scratch/stefan/7770550/working/building/REAL300000300548 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/790 `/scratch/stefan/7770550/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(F)C([N+](=O)[O-])=C1) `REAL300000300548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300548 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(F)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 2, 2, 2, 1] 17 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300548 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(F)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300548 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300548/1 /scratch/stefan/7770550/working/building/REAL300000300548 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/791 `/scratch/stefan/7770550/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(F)C([N+](=O)[O-])=C1) `REAL300000300548.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300548 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(F)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1] 17 rigid atoms, others: [35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300548 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C)=C(F)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 15, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 9, 9, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300548 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300548 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300548/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300548/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300548 Building REAL300000300549 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300549' /scratch/stefan/7770550/working/building/REAL300000300549 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300549 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300549/0 /scratch/stefan/7770550/working/building/REAL300000300549 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/792 `/scratch/stefan/7770550/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CN=C1Cl) `REAL300000300549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300549 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 21, 33, 33, 33, 33, 33, 21, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1] 33 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300549 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 17, 17, 17, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300549 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300549 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300549/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300549 Building REAL300000300550 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300550' /scratch/stefan/7770550/working/building/REAL300000300550 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300550 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300550/0 /scratch/stefan/7770550/working/building/REAL300000300550 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/793 `/scratch/stefan/7770550/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C(C)C)C=N1) `REAL300000300550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300550 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C(C)C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 19, 28, 31, 31, 31, 31, 19, 7, 1, 7, 7, 1, 1, 1, 1, 6, 6, 1, 1, 31, 31, 31, 31, 31, 31, 1, 6, 7, 7, 7, 7, 7, 7, 1] 39 rigid atoms, others: [36, 11, 14, 15, 16, 17, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300550 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C(C)C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 31, 31, 31, 39, 39, 31, 31, 2, 2, 2, 1, 1, 1, 31, 39, 39, 39, 39, 39, 39, 39, 31] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300550 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300550 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300550/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300550 Building REAL300000300551 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300551' /scratch/stefan/7770550/working/building/REAL300000300551 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300551 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300551/0 /scratch/stefan/7770550/working/building/REAL300000300551 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/794 `/scratch/stefan/7770550/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300551 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 17, 45, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 45, 45, 45, 17, 17, 1, 1, 1, 2, 2, 2, 17] 45 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300551 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 5, 5, 5, 1, 1, 17, 17, 17, 17, 17, 17, 1] 45 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 22, 23, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300551 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300551/1 /scratch/stefan/7770550/working/building/REAL300000300551 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/795 `/scratch/stefan/7770550/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300551.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300551 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 17, 46, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 46, 46, 46, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 46 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300551 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 5, 5, 5, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 46 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 36, 27, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300551 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300551 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300551/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300551/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300551 Building REAL300000300552 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300552' /scratch/stefan/7770550/working/building/REAL300000300552 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300552 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300552/0 /scratch/stefan/7770550/working/building/REAL300000300552 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/796 `/scratch/stefan/7770550/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C=C1Cl) `REAL300000300552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300552 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300552 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300552 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300552 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300552/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300552 Building REAL300000300553 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300553' /scratch/stefan/7770550/working/building/REAL300000300553 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300553 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300553/0 /scratch/stefan/7770550/working/building/REAL300000300553 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/797 `/scratch/stefan/7770550/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1C(=O)[O-]) `REAL300000300553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300553 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 2, 2, 2, 15, 15, 15] 15 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300553 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 15, 15, 9, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 9, 15, 15, 15, 15, 15, 15, 2, 2, 2] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300553 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300553 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300553/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300553 Building REAL300000300554 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300554' /scratch/stefan/7770550/working/building/REAL300000300554 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300554 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300554/0 /scratch/stefan/7770550/working/building/REAL300000300554 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/798 `/scratch/stefan/7770550/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C3=C(C=CC=C31)C(=O)N2C) `REAL300000300554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300554 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C3=C(C=CC=C31)C(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 13, 21, 21, 21, 21, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 13, 1, 1, 1, 1, 1, 2, 2, 2] 21 rigid atoms, others: [35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300554 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C3=C(C=CC=C31)C(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 33, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300554 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300554/1 /scratch/stefan/7770550/working/building/REAL300000300554 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/799 `/scratch/stefan/7770550/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C3=C(C=CC=C31)C(=O)N2C) `REAL300000300554.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300554 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C3=C(C=CC=C31)C(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 21, 21, 21, 21, 21, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 2, 2, 2] 21 rigid atoms, others: [34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300554 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C3=C(C=CC=C31)C(=O)N2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 10, 32, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300554 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300554 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300554/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300554/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300554 Building REAL300000300555 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300555' /scratch/stefan/7770550/working/building/REAL300000300555 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300555 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300555/0 /scratch/stefan/7770550/working/building/REAL300000300555 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/800 `/scratch/stefan/7770550/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F) `REAL300000300555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300555 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 17, 17, 39, 39, 39, 39, 17, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 1] 39 rigid atoms, others: [35, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300555 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 1, 39, 39, 39, 39, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300555 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300555/1 /scratch/stefan/7770550/working/building/REAL300000300555 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/801 `/scratch/stefan/7770550/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F) `REAL300000300555.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300555 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 17, 35, 43, 43, 43, 43, 17, 7, 1, 7, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 17, 1, 2, 2, 2, 1] 43 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300555 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 19, 19, 19, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 1, 1, 1, 7, 43, 43, 43, 43, 43] 43 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300555 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300555 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300555/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300555/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300555 Building REAL300000300556 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300556' /scratch/stefan/7770550/working/building/REAL300000300556 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300556 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300556/0 /scratch/stefan/7770550/working/building/REAL300000300556 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/802 `/scratch/stefan/7770550/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1Cl) `REAL300000300556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300556 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 10, 11, 18, 18, 18, 18, 10, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2] 18 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300556 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1, 1, 1, 18, 18, 18, 18, 18] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300556 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300556/1 /scratch/stefan/7770550/working/building/REAL300000300556 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/803 `/scratch/stefan/7770550/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1Cl) `REAL300000300556.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300556 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 21, 21, 21, 21, 21, 11, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 11, 1, 1, 2, 2, 2] 21 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300556 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300556 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300556 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300556/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300556/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300556 Building REAL300000300557 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300557' /scratch/stefan/7770550/working/building/REAL300000300557 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300557 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300557/0 /scratch/stefan/7770550/working/building/REAL300000300557 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/804 `/scratch/stefan/7770550/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300557 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 37] 37 rigid atoms, others: [13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300557 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 13, 37, 37, 13, 14, 37, 37, 37, 37, 37, 1, 2, 2, 2, 1, 37, 37, 37, 37, 37, 37, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 35, 24, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300557 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300557/1 /scratch/stefan/7770550/working/building/REAL300000300557 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/805 `/scratch/stefan/7770550/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300557.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300557 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 7, 1, 1, 1, 2, 2, 2, 33] 33 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300557 none CC1=CC(C(=O)[O-])=C(F)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 13, 33, 33, 13, 27, 33, 33, 33, 33, 33, 1, 2, 2, 2, 1, 13, 33, 33, 33, 33, 33, 33, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 36, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300557 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300557 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300557/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300557/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300557 Building REAL300000300558 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300558' /scratch/stefan/7770550/working/building/REAL300000300558 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300558 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300558/0 /scratch/stefan/7770550/working/building/REAL300000300558 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/806 `/scratch/stefan/7770550/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C(F)=C(F)C(F)=C1F) `REAL300000300558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300558 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C(F)=C(F)C(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 15, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300558 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C(F)=C(F)C(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 15, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 26, 26, 26, 26, 24, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300558 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300558 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300558/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300558 Building REAL300000300559 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300559' /scratch/stefan/7770550/working/building/REAL300000300559 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300559 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300559/0 /scratch/stefan/7770550/working/building/REAL300000300559 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/807 `/scratch/stefan/7770550/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300559 none CCC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 17, 93, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 93, 93, 93, 93, 93, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 93 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300559 none CCC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 1, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 18, 18, 18, 18, 18, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 93 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 39, 23, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300559 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300559/1 /scratch/stefan/7770550/working/building/REAL300000300559 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/808 `/scratch/stefan/7770550/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300559.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300559 none CCC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 65, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 65, 65, 65, 65, 65, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 65 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 180 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300559 none CCC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 20, 20, 20, 20, 20, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1] 65 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 38, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300559 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300559 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300559/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300559/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300559 Building REAL300000300560 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300560' /scratch/stefan/7770550/working/building/REAL300000300560 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300560 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300560/0 /scratch/stefan/7770550/working/building/REAL300000300560 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/809 `/scratch/stefan/7770550/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300560 none COCCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 79, 21, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 87, 87, 87, 87, 87, 79, 79, 21, 1, 1, 1, 2, 2, 2, 21] 87 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300560 none COCCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [27, 14, 8, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 17, 17, 21, 21, 21, 21, 21, 1, 1, 27, 27, 27, 14, 14, 8, 8, 1, 21, 21, 21, 21, 21, 21, 1] 87 rigid atoms, others: [3, 4, 5, 6, 7, 21, 22, 30, 37] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300560 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300560 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300560/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300560 Building REAL300000300561 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300561' /scratch/stefan/7770550/working/building/REAL300000300561 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300561 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300561/0 /scratch/stefan/7770550/working/building/REAL300000300561 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/810 `/scratch/stefan/7770550/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C([N+](=O)[O-])=N1) `REAL300000300561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300561 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 20, 20, 20, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 20, 20, 20, 20, 20, 28, 28, 28, 28, 28, 20, 1, 1, 1, 2, 2, 2] 28 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300561 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 4, 4, 4, 6, 20, 20, 6, 6, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 20, 20, 20, 20, 20, 20] 28 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300561 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300561 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300561/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300561 Building REAL300000300562 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300562' /scratch/stefan/7770550/working/building/REAL300000300562 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300562 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300562/0 /scratch/stefan/7770550/working/building/REAL300000300562 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/811 `/scratch/stefan/7770550/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1Br) `REAL300000300562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300562 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 7, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300562 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300562 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300562/1 /scratch/stefan/7770550/working/building/REAL300000300562 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/812 `/scratch/stefan/7770550/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1Br) `REAL300000300562.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300562 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 9, 13, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300562 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300562 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300562 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300562/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300562/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300562 Building REAL300000300563 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300563' /scratch/stefan/7770550/working/building/REAL300000300563 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300563 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300563/0 /scratch/stefan/7770550/working/building/REAL300000300563 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/813 `/scratch/stefan/7770550/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C)=C1Br) `REAL300000300563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300563 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 2, 2, 2] 11 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300563 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300563 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300563/1 /scratch/stefan/7770550/working/building/REAL300000300563 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/814 `/scratch/stefan/7770550/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C)=C1Br) `REAL300000300563.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300563 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2] 11 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300563 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300563 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300563 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300563/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300563/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300563 Building REAL300000300564 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300564' /scratch/stefan/7770550/working/building/REAL300000300564 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300564 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300564/0 /scratch/stefan/7770550/working/building/REAL300000300564 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/815 `/scratch/stefan/7770550/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-]) `REAL300000300564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300564 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 9, 9, 9, 9, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 17, 17, 25, 25, 25, 25, 25, 9, 9, 5, 1, 1, 1, 2, 2, 2, 9] 25 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300564 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 1, 1, 5, 9, 9, 9, 9, 9, 9, 1] 25 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300564 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300564 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300564/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300564 Building REAL300000300565 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300565' /scratch/stefan/7770550/working/building/REAL300000300565 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300565 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300565/0 /scratch/stefan/7770550/working/building/REAL300000300565 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/816 `/scratch/stefan/7770550/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCOCC2)N=C1) `REAL300000300565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300565 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCOCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 17, 17, 17, 17, 17, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 85 rigid atoms, others: [41, 11, 14, 15, 16, 17, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300565 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCOCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 85, 85, 85, 85, 85, 17, 17, 2, 2, 2, 1, 1, 1, 17, 85, 85, 85, 85, 85, 85, 85, 85, 85, 17] 85 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300565 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCOCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 85, 85, 85, 85, 43, 13, 7, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 85, 85, 85, 85, 85, 85, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7] 85 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41]) total number of confs: 170 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300565 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300565 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300565/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300565 Building REAL300000300566 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300566' /scratch/stefan/7770550/working/building/REAL300000300566 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300566 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300566/0 /scratch/stefan/7770550/working/building/REAL300000300566 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/817 `/scratch/stefan/7770550/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N(C)C1CCCC1) `REAL300000300566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300566 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N(C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 17, 26, 26, 26, 26, 26, 17, 7, 4, 7, 7, 1, 4, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 120 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300566 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N(C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300566 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300566 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300566/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300566 Building REAL300000300567 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300567' /scratch/stefan/7770550/working/building/REAL300000300567 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300567 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300567/0 /scratch/stefan/7770550/working/building/REAL300000300567 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/818 `/scratch/stefan/7770550/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCC2(CCCCC2)CC1) `REAL300000300567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300567 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCC2(CCCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 24, 27, 27, 27, 27, 16, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 128 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300567 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCC2(CCCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 20, 20, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300567 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300567 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300567/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300567 Building REAL300000300568 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300568' /scratch/stefan/7770550/working/building/REAL300000300568 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300568 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300568/0 /scratch/stefan/7770550/working/building/REAL300000300568 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/819 `/scratch/stefan/7770550/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C=C1Cl) `REAL300000300568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300568 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 9, 15, 15, 15, 15, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 1] 15 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300568 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300568 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300568/1 /scratch/stefan/7770550/working/building/REAL300000300568 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/820 `/scratch/stefan/7770550/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1Cl) `REAL300000300568.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300568 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 11, 15, 15, 15, 15, 15, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300568 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300568 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300568 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300568/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300568/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300568 Building REAL300000300569 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300569' /scratch/stefan/7770550/working/building/REAL300000300569 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300569 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300569/0 /scratch/stefan/7770550/working/building/REAL300000300569 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/821 `/scratch/stefan/7770550/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C([O-])C=C1C) `REAL300000300569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300569 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C([O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300569 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C([O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300569 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300569 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300569/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300569 Building REAL300000300570 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300570' /scratch/stefan/7770550/working/building/REAL300000300570 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300570 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300570/0 /scratch/stefan/7770550/working/building/REAL300000300570 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/822 `/scratch/stefan/7770550/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(C)(C)C)S1) `REAL300000300570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300570 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 6, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 21, 21, 21, 21, 21, 21, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 41 rigid atoms, others: [11, 14, 15, 16, 17, 18, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300570 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 41, 41, 41, 21, 2, 2, 2, 1, 1, 1, 21, 21, 41, 41, 41, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300570 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300570 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300570/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300570 Building REAL300000300571 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300571' /scratch/stefan/7770550/working/building/REAL300000300571 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300571 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300571/0 /scratch/stefan/7770550/working/building/REAL300000300571 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/823 `/scratch/stefan/7770550/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300571 none CCCN1C=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 36, 36, 36, 36, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 36, 86, 86, 86, 86, 86, 86, 86, 36, 1, 1, 1, 2, 2, 2, 36] 86 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300571 none CCCN1C=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 36, 36, 17, 24, 36, 36, 36, 36, 36, 1, 14, 14, 14, 14, 14, 6, 6, 1, 36, 36, 36, 36, 36, 36, 1] 86 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 36, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300571 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300571 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300571/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300571 Building REAL300000300572 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300572' /scratch/stefan/7770550/working/building/REAL300000300572 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300572 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300572/0 /scratch/stefan/7770550/working/building/REAL300000300572 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/824 `/scratch/stefan/7770550/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCOC2)N=C1) `REAL300000300572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300572 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCOC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 17, 17, 17, 17, 17, 17, 1, 7, 7, 7, 7, 7, 7, 7, 1] 73 rigid atoms, others: [38, 11, 14, 15, 16, 17, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300572 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCOC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 73, 73, 73, 73, 17, 17, 2, 2, 2, 1, 1, 1, 17, 73, 73, 73, 73, 73, 73, 73, 17] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 196 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300572 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCOC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 12, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 39, 39, 73, 73, 73, 73, 39, 13, 7, 13, 13, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 73, 73, 73, 73, 73, 73, 7, 1, 1, 1, 1, 1, 1, 1, 7] 73 rigid atoms, others: [32, 33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 386 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300572 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300572 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300572/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300572 Building REAL300000300573 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300573' /scratch/stefan/7770550/working/building/REAL300000300573 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300573 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300573/0 /scratch/stefan/7770550/working/building/REAL300000300573 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/825 `/scratch/stefan/7770550/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(F)F)C=C1) `REAL300000300573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300573 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 23, 23, 1, 1, 5, 5, 5, 5, 5, 5, 3, 1, 1, 20, 20, 23, 1, 1] 49 rigid atoms, others: [32, 33, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 89 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300573 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 19, 49, 49, 49, 5, 5, 2, 2, 2, 1, 1, 1, 5, 5, 5, 49, 49, 49, 5, 5] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 167 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300573 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300573 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300573/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300573 Building REAL300000300574 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300574' /scratch/stefan/7770550/working/building/REAL300000300574 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300574 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300574/0 /scratch/stefan/7770550/working/building/REAL300000300574 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/826 `/scratch/stefan/7770550/working/3D/826' -> `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)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300574 none COC(=O)C1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 26, 40, 26, 26, 26, 26, 26, 26, 26, 26, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 40, 40, 40, 26, 26, 26, 1, 1, 1, 2, 2, 2] 40 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300574 none COC(=O)C1=CC([N+](=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 26, 26, 15, 20, 26, 26, 26, 26, 26, 5, 5, 5, 1, 1, 1, 26, 26, 26, 26, 26, 26] 40 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300574 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300574 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300574/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300574 Building REAL300000300575 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300575' /scratch/stefan/7770550/working/building/REAL300000300575 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300575 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300575/0 /scratch/stefan/7770550/working/building/REAL300000300575 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/827 `/scratch/stefan/7770550/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C)=C1F) `REAL300000300575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300575 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 13, 13, 27, 27, 27, 27, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300575 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 19, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300575 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300575/1 /scratch/stefan/7770550/working/building/REAL300000300575 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/828 `/scratch/stefan/7770550/working/3D/828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C)=C1F) `REAL300000300575.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300575 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 23, 29, 29, 29, 29, 29, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1, 2, 2, 2] 29 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300575 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 29, 29, 19, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300575 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300575 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300575/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300575/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300575 Building REAL300000300576 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300576' /scratch/stefan/7770550/working/building/REAL300000300576 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300576 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300576/0 /scratch/stefan/7770550/working/building/REAL300000300576 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/829 `/scratch/stefan/7770550/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300576 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 54, 54, 54, 54, 54, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 54 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300576 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 5, 5, 5, 5, 5, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 54 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 22, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300576 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300576/1 /scratch/stefan/7770550/working/building/REAL300000300576 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/830 `/scratch/stefan/7770550/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300576.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300576 none CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 54, 54, 54, 54, 54, 17, 17, 1, 1, 1, 2, 2, 2, 17] 54 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300576 none CCOC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 5, 5, 1, 1, 17, 17, 17, 17, 17, 17, 1] 54 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 22, 36, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300576 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300576 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300576/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300576/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300576 Building REAL300000300577 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300577' /scratch/stefan/7770550/working/building/REAL300000300577 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300577 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300577/0 /scratch/stefan/7770550/working/building/REAL300000300577 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/831 `/scratch/stefan/7770550/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN2CCCCC2=N1) `REAL300000300577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300577 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN2CCCCC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 17, 19, 19, 19, 19, 19, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300577 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN2CCCCC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300577 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300577 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300577/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300577 Building REAL300000300578 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300578' /scratch/stefan/7770550/working/building/REAL300000300578 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300578 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300578/0 /scratch/stefan/7770550/working/building/REAL300000300578 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/832 `/scratch/stefan/7770550/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1CC(=O)[O-]) `REAL300000300578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300578 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 16, 16, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 24, 40, 40, 17, 17, 17, 16, 16, 5, 1, 1, 1, 2, 2, 2, 16, 24, 24] 40 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300578 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 16, 16, 9, 16, 16, 16, 16, 16, 16, 1, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 9, 16, 16, 16, 16, 16, 16, 1, 3, 3] 40 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300578 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300578 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300578/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300578 Building REAL300000300579 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300579' /scratch/stefan/7770550/working/building/REAL300000300579 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300579 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300579/0 /scratch/stefan/7770550/working/building/REAL300000300579 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/833 `/scratch/stefan/7770550/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300579 none COCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 21, 21, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 41, 41, 41, 41, 41, 21, 21, 7, 1, 1, 1, 2, 2, 2, 21, 21] 41 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300579 none COCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 17, 17, 21, 21, 21, 21, 21, 1, 1, 8, 8, 8, 4, 4, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1, 1] 41 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 22, 38, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300579 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300579 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300579/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300579 Building REAL300000300580 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300580' /scratch/stefan/7770550/working/building/REAL300000300580 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300580 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300580/0 /scratch/stefan/7770550/working/building/REAL300000300580 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/834 `/scratch/stefan/7770550/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300580 none COC1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 43, 43, 43, 43, 43, 43, 86, 1, 1, 1, 2, 2, 2, 43] 86 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300580 none COC1=CC=C(O)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 43, 43, 20, 20, 43, 43, 43, 43, 43, 1, 3, 3, 3, 1, 1, 2, 43, 43, 43, 43, 43, 43, 1] 86 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 35, 22, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300580 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300580/1 /scratch/stefan/7770550/working/building/REAL300000300580 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/835 `/scratch/stefan/7770550/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(O)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300580.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300580 none COC1=CC=C(O)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [49, 49, 49, 49, 49, 49, 49, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 98, 7, 1, 1, 1, 2, 2, 2, 49] 98 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300580 none COC1=CC=C(O)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 24, 49, 49, 24, 43, 49, 49, 49, 49, 49, 1, 3, 3, 3, 1, 1, 2, 24, 49, 49, 49, 49, 49, 49, 1] 98 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 36, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300580 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300580 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300580/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300580/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300580 Building REAL300000300581 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300581' /scratch/stefan/7770550/working/building/REAL300000300581 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300581 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300581/0 /scratch/stefan/7770550/working/building/REAL300000300581 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/836 `/scratch/stefan/7770550/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C)=C1Cl) `REAL300000300581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300581 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 9, 15, 15, 15, 15, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 1, 2, 2, 2] 15 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300581 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 13, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 13, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300581 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300581/1 /scratch/stefan/7770550/working/building/REAL300000300581 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/837 `/scratch/stefan/7770550/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C)=C1Cl) `REAL300000300581.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300581 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 12, 16, 16, 16, 16, 16, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 9, 1, 1, 1, 2, 2, 2] 16 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300581 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 16, 16, 14, 16, 16, 16, 16, 2, 2, 2, 1, 1, 1, 7, 16, 16, 15, 16, 16, 16] 16 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300581 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300581 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300581/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300581/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300581 Building REAL300000300582 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300582' /scratch/stefan/7770550/working/building/REAL300000300582 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300582 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300582/0 /scratch/stefan/7770550/working/building/REAL300000300582 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/838 `/scratch/stefan/7770550/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C)O1) `REAL300000300582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300582 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21, 21, 21] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 21, 22, 23, 24, 33, 28, 29, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300582 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 7, 7, 7, 17, 21, 21, 17, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 1, 21, 21, 21, 21, 21, 21, 2, 2, 2] 21 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300582 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300582/1 /scratch/stefan/7770550/working/building/REAL300000300582 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/839 `/scratch/stefan/7770550/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(C)O1) `REAL300000300582.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300582 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 2, 2, 2, 21, 21, 21] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300582 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 5, 5, 5, 13, 21, 21, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 1, 13, 21, 21, 21, 21, 21, 21, 2, 2, 2] 21 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300582 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300582 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300582/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300582/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300582 Building REAL300000300583 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300583' /scratch/stefan/7770550/working/building/REAL300000300583 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300583 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300583/0 /scratch/stefan/7770550/working/building/REAL300000300583 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/840 `/scratch/stefan/7770550/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1NC(=O)CO2) `REAL300000300583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300583 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1NC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 16, 22, 24, 24, 24, 24, 16, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300583 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1NC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 1, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300583 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300583/1 /scratch/stefan/7770550/working/building/REAL300000300583 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/841 `/scratch/stefan/7770550/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1NC(=O)CO2) `REAL300000300583.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300583 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1NC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 15, 23, 23, 23, 23, 23, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 15, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300583 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1NC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300583 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300583 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300583/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300583/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300583 Building REAL300000300584 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300584' /scratch/stefan/7770550/working/building/REAL300000300584 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300584 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300584/0 /scratch/stefan/7770550/working/building/REAL300000300584 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/842 `/scratch/stefan/7770550/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCCC2=C1) `REAL300000300584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300584 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300584 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300584 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300584 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300584/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300584 Building REAL300000300585 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300585' /scratch/stefan/7770550/working/building/REAL300000300585 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300585 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300585/0 /scratch/stefan/7770550/working/building/REAL300000300585 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/843 `/scratch/stefan/7770550/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)CC1) `REAL300000300585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300585 none COC(=O)C1(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 9, 19, 19, 19, 19, 19, 1, 1, 5, 5, 12, 12, 12, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1, 5, 5, 5, 5] 90 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 40, 23, 24, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300585 none COC(=O)C1(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 5, 5, 1, 1, 9, 9, 9, 26, 52, 52, 26, 26, 52, 52, 52, 52, 52, 5, 5, 1, 1, 9, 9, 9, 5, 5, 26, 52, 52, 52, 52, 52, 52, 5, 5, 1, 1, 1, 1] 90 rigid atoms, others: [2, 4, 5, 42, 43, 44, 41, 25, 26] set([0, 1, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 331 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: REAL300000300585 none COC(=O)C1(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 52, 90, 19, 19, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 52, 52, 90, 90, 90, 19, 19, 5, 1, 1, 1, 2, 2, 2, 19, 19, 52, 52, 52, 52] 90 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 301 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300585 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300585 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300585/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300585 Building REAL300000300586 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300586' /scratch/stefan/7770550/working/building/REAL300000300586 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300586 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300586/0 /scratch/stefan/7770550/working/building/REAL300000300586 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/844 `/scratch/stefan/7770550/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300586 none CCOC(=O)C1=CC(F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 101, 17, 101, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 119, 119, 119, 119, 119, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 119 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300586 none CCOC(=O)C1=CC(F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [24, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 24, 24, 24, 24, 24, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 119 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 40, 25, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300586 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300586/1 /scratch/stefan/7770550/working/building/REAL300000300586 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/845 `/scratch/stefan/7770550/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300586.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300586 none CCOC(=O)C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 91, 17, 91, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 101, 101, 101, 101, 101, 17, 17, 1, 1, 1, 2, 2, 2, 17] 101 rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300586 none CCOC(=O)C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 19, 19, 19, 18, 18, 1, 1, 17, 17, 17, 17, 17, 17, 1] 101 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 25, 39, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300586 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300586 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300586/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300586/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300586 Building REAL300000300587 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300587' /scratch/stefan/7770550/working/building/REAL300000300587 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300587 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300587/0 /scratch/stefan/7770550/working/building/REAL300000300587 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/846 `/scratch/stefan/7770550/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300587 none COCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 29, 29, 17, 29, 29, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 29, 22, 29, 29, 7, 1, 1, 1, 2, 2, 2] 50 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300587 none COCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 29, 29, 19, 23, 29, 29, 29, 29, 29, 12, 12, 12, 6, 6, 1, 1, 1, 1, 13, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300587 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300587/1 /scratch/stefan/7770550/working/building/REAL300000300587 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/847 `/scratch/stefan/7770550/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300587.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300587 none COCC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 36, 36, 36, 36, 36, 36, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 39, 39, 39, 39, 39, 36, 36, 36, 36, 1, 1, 1, 2, 2, 2] 39 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300587 none COCC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 36, 36, 15, 15, 36, 36, 36, 36, 36, 10, 10, 10, 4, 4, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36] 39 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300587 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300587 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300587/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300587/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300587 Building REAL300000300588 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300588' /scratch/stefan/7770550/working/building/REAL300000300588 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300588 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300588/0 /scratch/stefan/7770550/working/building/REAL300000300588 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/848 `/scratch/stefan/7770550/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)OC)O1) `REAL300000300588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300588 none CCC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 29, 29, 29, 15, 25, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2, 15, 29, 29, 29] 29 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300588 none CCC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 7, 7, 7, 9, 15, 15, 9, 15, 15, 15, 15, 15, 15, 1, 1, 1, 7, 7, 7, 1, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 1, 7, 7, 7] 29 rigid atoms, others: [1, 2, 3, 4, 18, 19, 20, 24, 36] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300588 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300588/1 /scratch/stefan/7770550/working/building/REAL300000300588 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/849 `/scratch/stefan/7770550/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(C(=O)OC)O1) `REAL300000300588.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300588 none CCC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 12, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [69, 39, 39, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 39, 39, 39, 102, 102, 102, 39, 69, 69, 69, 69, 69, 7, 1, 1, 1, 2, 2, 2, 39, 102, 102, 102] 108 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 447 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300588 none CCC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 12, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 5, 5, 5, 15, 39, 39, 15, 23, 39, 39, 39, 39, 39, 1, 1, 1, 13, 13, 13, 1, 6, 6, 6, 6, 6, 15, 39, 39, 39, 39, 39, 39, 1, 13, 13, 13] 108 rigid atoms, others: [1, 2, 3, 4, 37, 18, 19, 20, 24] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300588 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300588 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300588/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300588/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300588 Building REAL300000300589 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300589' /scratch/stefan/7770550/working/building/REAL300000300589 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300589 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300589/0 /scratch/stefan/7770550/working/building/REAL300000300589 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/850 `/scratch/stefan/7770550/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)C=C1) `REAL300000300589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300589 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1] 47 rigid atoms, others: [32, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 118 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300589 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 47, 47, 47, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 47, 47, 47, 47, 47, 47, 47, 15, 15] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300589 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300589 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300589/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300589 Building REAL300000300590 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300590' /scratch/stefan/7770550/working/building/REAL300000300590 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300590 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300590/0 /scratch/stefan/7770550/working/building/REAL300000300590 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/851 `/scratch/stefan/7770550/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300590 none CC1=C(C)SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300590 none CC1=C(C)SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 21, 21, 19, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 20, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300590 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300590 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300590/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300590 Building REAL300000300591 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300591' /scratch/stefan/7770550/working/building/REAL300000300591 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300591 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300591/0 /scratch/stefan/7770550/working/building/REAL300000300591 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/852 `/scratch/stefan/7770550/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCOC2=C1) `REAL300000300591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300591 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300591 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300591 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300591 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300591/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300591 Building REAL300000300592 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300592' /scratch/stefan/7770550/working/building/REAL300000300592 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300592 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300592/0 /scratch/stefan/7770550/working/building/REAL300000300592 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/853 `/scratch/stefan/7770550/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC2=CC=CN=C21) `REAL300000300592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300592 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 23, 38, 38, 38, 38, 38, 23, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 2, 2, 2, 1, 1, 1, 1, 1] 38 rigid atoms, others: [34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300592 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 17, 17, 17, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300592 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300592/1 /scratch/stefan/7770550/working/building/REAL300000300592 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/854 `/scratch/stefan/7770550/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=CC2=CC=CN=C21) `REAL300000300592.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300592 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 23, 38, 38, 38, 38, 38, 23, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 23, 2, 2, 2, 1, 1, 1, 1, 1] 38 rigid atoms, others: [35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300592 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=CC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 17, 17, 17, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 2, 2, 2, 1, 1, 1, 8, 38, 38, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300592 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300592 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300592/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300592/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300592 Building REAL300000300593 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300593' /scratch/stefan/7770550/working/building/REAL300000300593 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300593 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300593/0 /scratch/stefan/7770550/working/building/REAL300000300593 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/855 `/scratch/stefan/7770550/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C1=CC=NO1) `REAL300000300593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300593 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 13, 19, 23, 23, 23, 23, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 13, 1, 1, 1, 1, 5, 5] 34 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300593 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 34, 34, 34, 34, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 23, 34, 34] 34 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300593 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 20, 26, 34, 34, 34, 34, 20, 14, 5, 14, 14, 5, 5, 2, 5, 5, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 20, 5, 2, 5, 5, 1, 1] 34 rigid atoms, others: [36, 37, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 170 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300593 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300593/1 /scratch/stefan/7770550/working/building/REAL300000300593 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/856 `/scratch/stefan/7770550/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C1=CC=NO1) `REAL300000300593.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300593 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 15, 29, 29, 29, 29, 29, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 7, 7] 45 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300593 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 29, 45, 45, 45, 45, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29, 45, 45] 45 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300593 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1C1=CC=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 29, 45, 45, 45, 45, 45, 27, 15, 7, 15, 15, 7, 7, 2, 7, 7, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 7, 6, 7, 7, 1, 1] 45 rigid atoms, others: [35, 36, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 173 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300593 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300593 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300593/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300593/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300593 Building REAL300000300594 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300594' /scratch/stefan/7770550/working/building/REAL300000300594 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300594 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300594/0 /scratch/stefan/7770550/working/building/REAL300000300594 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/857 `/scratch/stefan/7770550/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12) `REAL300000300594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300594 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 13, 13, 13, 13, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 13, 13, 7, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13] 25 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300594 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 13, 13, 7, 11, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 7, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 41, 42, 43, 44, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300594 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300594/1 /scratch/stefan/7770550/working/building/REAL300000300594 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/858 `/scratch/stefan/7770550/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12) `REAL300000300594.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300594 none CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 13, 13, 13, 13, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 24, 24, 24, 24, 13, 13, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13] 24 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300594 none CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 13, 13, 7, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 24 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 41, 42, 43, 40, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300594 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300594 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300594/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300594/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300594 Building REAL300000300595 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300595' /scratch/stefan/7770550/working/building/REAL300000300595 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300595 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300595/0 /scratch/stefan/7770550/working/building/REAL300000300595 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/859 `/scratch/stefan/7770550/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(F)(F)F)N=C1) `REAL300000300595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300595 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 9, 17, 19, 19, 19, 19, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 9, 9, 1] 88 rigid atoms, others: [33, 34, 37, 11, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300595 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OCC(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 19, 19, 19, 19, 56, 88, 88, 88, 88, 19, 19, 2, 2, 2, 1, 1, 1, 5, 19, 19, 88, 88, 19] 88 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300595 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300595/1 /scratch/stefan/7770550/working/building/REAL300000300595 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/860 `/scratch/stefan/7770550/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OCC(F)(F)F)N=C1) `REAL300000300595.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300595 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OCC(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 9, 14, 23, 23, 23, 23, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 13, 13, 1] 94 rigid atoms, others: [32, 33, 36, 11, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300595 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OCC(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 60, 94, 94, 94, 94, 23, 23, 2, 2, 2, 1, 1, 1, 23, 23, 94, 94, 23] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300595 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300595 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300595/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300595/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300595 Building REAL300000300596 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300596' /scratch/stefan/7770550/working/building/REAL300000300596 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300596 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300596/0 /scratch/stefan/7770550/working/building/REAL300000300596 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/861 `/scratch/stefan/7770550/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(F)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300596 none COC(=O)C1=CC(F)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 29, 45, 29, 29, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 45, 45, 45, 29, 29, 29, 1, 1, 1, 2, 2, 2] 45 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300596 none COC(=O)C1=CC(F)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 29, 29, 15, 25, 29, 29, 29, 29, 29, 5, 5, 5, 1, 1, 1, 29, 29, 29, 29, 29, 29] 45 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300596 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300596/1 /scratch/stefan/7770550/working/building/REAL300000300596 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/862 `/scratch/stefan/7770550/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(F)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300596.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300596 none COC(=O)C1=CC(F)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 35, 19, 19, 13, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300596 none COC(=O)C1=CC(F)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 9, 19, 19, 19, 19, 19, 19, 7, 7, 7, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300596 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300596 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300596/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300596/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300596 Building REAL300000300597 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300597' /scratch/stefan/7770550/working/building/REAL300000300597 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300597 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300597/0 /scratch/stefan/7770550/working/building/REAL300000300597 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/863 `/scratch/stefan/7770550/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(F)=C1) `REAL300000300597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300597 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300597 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300597 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300597/1 /scratch/stefan/7770550/working/building/REAL300000300597 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/864 `/scratch/stefan/7770550/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C(F)=C1) `REAL300000300597.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300597 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300597 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300597 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300597 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300597/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300597/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300597 Building REAL300000300598 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300598' /scratch/stefan/7770550/working/building/REAL300000300598 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300598 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300598/0 /scratch/stefan/7770550/working/building/REAL300000300598 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/865 `/scratch/stefan/7770550/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(C(=O)[O-])=C1C) `REAL300000300598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300598 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 15, 15, 15, 15, 15, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 15, 15, 15, 15, 15, 15, 9, 1, 1, 2, 2, 2] 15 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300598 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300598 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300598/1 /scratch/stefan/7770550/working/building/REAL300000300598 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/866 `/scratch/stefan/7770550/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(C(=O)[O-])=C1C) `REAL300000300598.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300598 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 13, 19, 19, 19, 19, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300598 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300598 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300598 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300598/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300598/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300598 Building REAL300000300599 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300599' /scratch/stefan/7770550/working/building/REAL300000300599 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300599 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300599/0 /scratch/stefan/7770550/working/building/REAL300000300599 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/867 `/scratch/stefan/7770550/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(Cl)=C1) `REAL300000300599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300599 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 16, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300599 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300599 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300599/1 /scratch/stefan/7770550/working/building/REAL300000300599 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/868 `/scratch/stefan/7770550/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(Cl)=C1) `REAL300000300599.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300599 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300599 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300599 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300599 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300599/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300599/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300599 Building REAL300000300600 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300600' /scratch/stefan/7770550/working/building/REAL300000300600 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300600 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300600/0 /scratch/stefan/7770550/working/building/REAL300000300600 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/869 `/scratch/stefan/7770550/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C)O1) `REAL300000300600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300600 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 43, 72, 43, 43, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 72, 72, 72, 43, 1, 1, 1, 2, 2, 2, 43, 43, 43] 72 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 212 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300600 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 1, 7, 7, 7, 19, 43, 43, 19, 31, 43, 43, 43, 43, 43, 1, 1, 1, 13, 13, 13, 1, 43, 43, 43, 43, 43, 43, 2, 2, 2] 72 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 224 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300600 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300600/1 /scratch/stefan/7770550/working/building/REAL300000300600 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/870 `/scratch/stefan/7770550/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(C)O1) `REAL300000300600.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300600 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 33, 61, 33, 33, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 33, 33, 33, 61, 61, 61, 33, 7, 1, 1, 1, 2, 2, 2, 33, 33, 33] 61 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300600 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 13, 33, 33, 13, 25, 33, 33, 33, 33, 33, 1, 1, 1, 11, 11, 11, 1, 13, 33, 33, 33, 33, 33, 33, 2, 2, 2] 61 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300600 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300600 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300600/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300600/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300600 Building REAL300000300601 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300601' /scratch/stefan/7770550/working/building/REAL300000300601 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300601 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300601/0 /scratch/stefan/7770550/working/building/REAL300000300601 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/871 `/scratch/stefan/7770550/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(Cl)=C1) `REAL300000300601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300601 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 16, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300601 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300601 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300601/1 /scratch/stefan/7770550/working/building/REAL300000300601 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/872 `/scratch/stefan/7770550/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(Cl)=C1) `REAL300000300601.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300601 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300601 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300601 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300601 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300601/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300601/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300601 Building REAL300000300602 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300602' /scratch/stefan/7770550/working/building/REAL300000300602 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300602 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300602/0 /scratch/stefan/7770550/working/building/REAL300000300602 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/873 `/scratch/stefan/7770550/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(Cl)C(C(=O)[O-])=C1) `REAL300000300602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300602 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 5, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 5, 1, 2, 2, 2, 1] 9 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300602 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C)=C(Cl)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 16, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300602 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300602 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300602/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300602 Building REAL300000300603 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300603' /scratch/stefan/7770550/working/building/REAL300000300603 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300603 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300603/0 /scratch/stefan/7770550/working/building/REAL300000300603 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/874 `/scratch/stefan/7770550/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N=C1C) `REAL300000300603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300603 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 25, 25, 25, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 41, 41, 41, 41, 41, 25, 1, 1, 1, 2, 2, 2, 25, 25, 25] 41 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 170 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300603 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 6, 6, 6, 19, 25, 25, 19, 23, 25, 25, 25, 25, 25, 1, 1, 1, 5, 5, 5, 5, 5, 1, 25, 25, 25, 25, 25, 25, 2, 2, 2] 41 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 27] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300603 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300603 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300603/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300603 Building REAL300000300604 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300604' /scratch/stefan/7770550/working/building/REAL300000300604 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300604 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300604/0 /scratch/stefan/7770550/working/building/REAL300000300604 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/875 `/scratch/stefan/7770550/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Br)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300604 none CC1=CC=C(Br)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 7, 1, 1, 1, 2, 2, 2, 11] 11 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 34, 33, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300604 none CC1=CC=C(Br)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 11, 11, 5, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 1, 1, 5, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300604 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300604/1 /scratch/stefan/7770550/working/building/REAL300000300604 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/876 `/scratch/stefan/7770550/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Br)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300604.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300604 none CC1=CC=C(Br)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 11] 11 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300604 none CC1=CC=C(Br)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 17, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 11, 11, 5, 5, 11, 11, 11, 11, 11, 1, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300604 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300604 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300604/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300604/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300604 Building REAL300000300605 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300605' /scratch/stefan/7770550/working/building/REAL300000300605 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300605 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300605/0 /scratch/stefan/7770550/working/building/REAL300000300605 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/877 `/scratch/stefan/7770550/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300605 none CC1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 13, 15, 15, 15, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 1, 2, 2, 2, 15] 15 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300605 none CC1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 15, 15, 9, 11, 15, 15, 15, 15, 15, 1, 2, 2, 2, 1, 1, 15, 15, 15, 15, 15, 15, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300605 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300605/1 /scratch/stefan/7770550/working/building/REAL300000300605 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/878 `/scratch/stefan/7770550/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300605.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300605 none CC1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 13, 15, 15, 15, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 2, 2, 2, 15] 15 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 34, 33, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300605 none CC1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 15, 15, 9, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 1, 1, 9, 15, 15, 15, 15, 15, 15, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300605 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300605 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300605/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300605/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300605 Building REAL300000300606 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300606' /scratch/stefan/7770550/working/building/REAL300000300606 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300606 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300606/0 /scratch/stefan/7770550/working/building/REAL300000300606 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/879 `/scratch/stefan/7770550/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-]) `REAL300000300606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300606 none CCN1C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 15, 15, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 29, 29, 29, 29, 29, 15, 7, 1, 1, 1, 2, 2, 2, 15] 29 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300606 none CCN1C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 7, 13, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 7, 15, 15, 15, 15, 15, 15, 1] 29 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 29, 37] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300606 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300606/1 /scratch/stefan/7770550/working/building/REAL300000300606 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/880 `/scratch/stefan/7770550/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-]) `REAL300000300606.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300606 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 17, 17, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 31, 31, 31, 31, 31, 17, 1, 1, 1, 2, 2, 2, 17] 31 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300606 none CCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 3, 3, 3, 7, 17, 17, 7, 7, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 17, 17, 17, 17, 17, 17, 1] 31 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 36, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300606 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300606 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300606/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300606/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300606 Building REAL300000300607 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300607' /scratch/stefan/7770550/working/building/REAL300000300607 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300607 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300607/0 /scratch/stefan/7770550/working/building/REAL300000300607 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/881 `/scratch/stefan/7770550/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=COC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300607 none COC(=O)C1=COC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 43, 57, 43, 43, 43, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 43, 57, 57, 57, 43, 1, 1, 1, 2, 2, 2, 43] 57 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300607 none COC(=O)C1=COC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [10, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 6, 21, 43, 43, 21, 34, 43, 43, 43, 43, 43, 1, 11, 11, 11, 1, 43, 43, 43, 43, 43, 43, 1] 57 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 22, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300607 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300607 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300607/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300607 Building REAL300000300608 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300608' /scratch/stefan/7770550/working/building/REAL300000300608 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300608 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300608/0 /scratch/stefan/7770550/working/building/REAL300000300608 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/882 `/scratch/stefan/7770550/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C(CC)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300608 none CCC1=NN(C)C(CC)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [60, 49, 49, 49, 49, 49, 49, 49, 73, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 60, 60, 60, 60, 60, 49, 49, 49, 73, 73, 73, 73, 73, 1, 1, 1, 2, 2, 2] 86 rigid atoms, others: [37, 38, 39, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 326 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300608 none CCC1=NN(C)C(CC)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 10, 10, 10, 24, 49, 49, 24, 40, 49, 49, 49, 49, 49, 6, 6, 6, 5, 5, 2, 2, 2, 2, 2, 3, 3, 3, 49, 49, 49, 49, 49, 49] 86 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10] set([0, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300608 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300608 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300608/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300608 Building REAL300000300609 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300609' /scratch/stefan/7770550/working/building/REAL300000300609 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300609 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300609/0 /scratch/stefan/7770550/working/building/REAL300000300609 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/883 `/scratch/stefan/7770550/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C) `REAL300000300609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300609 none CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 113, 102, 21, 102, 21, 21, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 115, 115, 115, 115, 115, 21, 5, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21] 115 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300609 none CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [15, 11, 6, 1, 6, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 1, 16, 16, 16, 15, 15, 1, 9, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2] 115 rigid atoms, others: [3, 5, 6, 7, 8, 22, 23, 24, 38, 30] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300609 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300609/1 /scratch/stefan/7770550/working/building/REAL300000300609 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/884 `/scratch/stefan/7770550/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C) `REAL300000300609.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300609 none CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 93, 23, 93, 23, 23, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 23, 23, 23, 107, 107, 107, 107, 107, 23, 1, 1, 1, 2, 2, 2, 23, 23, 23, 23] 107 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300609 none CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 6, 1, 6, 1, 1, 1, 1, 3, 3, 3, 9, 23, 23, 9, 10, 23, 23, 23, 23, 23, 1, 1, 1, 19, 19, 19, 18, 18, 1, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2] 107 rigid atoms, others: [3, 5, 6, 7, 8, 22, 23, 24, 30, 37] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300609 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300609 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300609/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300609/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300609 Building REAL300000300610 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300610' /scratch/stefan/7770550/working/building/REAL300000300610 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300610 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300610/0 /scratch/stefan/7770550/working/building/REAL300000300610 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/885 `/scratch/stefan/7770550/working/3D/885' -> `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)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300610 none CC1=CC([N+](=O)[O-])=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 1, 1, 2, 2, 2, 13] 13 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 53 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300610 none CC1=CC([N+](=O)[O-])=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 5, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 1, 2, 2, 2, 5, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 39, 24, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300610 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300610/1 /scratch/stefan/7770550/working/building/REAL300000300610 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/886 `/scratch/stefan/7770550/working/3D/886' -> `1.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)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300610.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300610 none CC1=CC([N+](=O)[O-])=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 11] 11 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300610 none CC1=CC([N+](=O)[O-])=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 11, 11, 5, 5, 11, 11, 11, 11, 11, 1, 2, 2, 2, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 38, 7, 8, 9, 10, 24, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300610 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300610 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300610/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300610/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300610 Building REAL300000300611 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300611' /scratch/stefan/7770550/working/building/REAL300000300611 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300611 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300611/0 /scratch/stefan/7770550/working/building/REAL300000300611 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/887 `/scratch/stefan/7770550/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1Cl) `REAL300000300611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300611 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 21, 21, 31, 31, 31, 31, 21, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 1, 1, 1] 31 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300611 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 31, 31, 31, 24, 31, 31, 31, 2, 2, 2, 1, 1, 1, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300611 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300611 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300611/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300611 Building REAL300000300612 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300612' /scratch/stefan/7770550/working/building/REAL300000300612 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300612 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300612/0 /scratch/stefan/7770550/working/building/REAL300000300612 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/888 `/scratch/stefan/7770550/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(Cl)=N1) `REAL300000300612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300612 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2] 11 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300612 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 11, 11, 5, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300612 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300612/1 /scratch/stefan/7770550/working/building/REAL300000300612 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/889 `/scratch/stefan/7770550/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(Cl)=N1) `REAL300000300612.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300612 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 7, 1, 1, 1, 2, 2, 2] 11 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300612 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 16, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 11, 11, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 1, 5, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300612 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300612 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300612/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300612/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300612 Building REAL300000300613 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300613' /scratch/stefan/7770550/working/building/REAL300000300613 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300613 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300613/0 /scratch/stefan/7770550/working/building/REAL300000300613 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/890 `/scratch/stefan/7770550/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C#N)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300613 none COC1=CC(C#N)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 39, 39, 39, 39, 39, 39, 39, 39, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 41, 41, 41, 39, 39, 39, 1, 1, 1, 2, 2, 2] 41 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300613 none COC1=CC(C#N)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 39, 39, 25, 37, 39, 39, 39, 39, 39, 4, 4, 4, 1, 1, 1, 39, 39, 39, 39, 39, 39] 41 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300613 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300613/1 /scratch/stefan/7770550/working/building/REAL300000300613 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/891 `/scratch/stefan/7770550/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C#N)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300613.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300613 none COC1=CC(C#N)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 29, 35, 35, 35, 35, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 5, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300613 none COC1=CC(C#N)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 35, 35, 29, 31, 35, 35, 35, 35, 35, 4, 4, 4, 1, 1, 1, 19, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300613 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300613 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300613/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300613/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300613 Building REAL300000300614 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300614' /scratch/stefan/7770550/working/building/REAL300000300614 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300614 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300614/0 /scratch/stefan/7770550/working/building/REAL300000300614 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/892 `/scratch/stefan/7770550/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C2=CC=CN=C21) `REAL300000300614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300614 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 13, 23, 25, 25, 25, 25, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1] 25 rigid atoms, others: [33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 32, 27, 28, 29, 30, 31]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300614 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C([N+](=O)[O-])C2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300614 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300614/1 /scratch/stefan/7770550/working/building/REAL300000300614 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/893 `/scratch/stefan/7770550/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C2=CC=CN=C21) `REAL300000300614.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300614 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 21, 23, 23, 23, 23, 23, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 13, 1, 1, 1, 1, 1] 23 rigid atoms, others: [34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300614 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C([N+](=O)[O-])C2=CC=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300614 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300614 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300614/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300614/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300614 Building REAL300000300615 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300615' /scratch/stefan/7770550/working/building/REAL300000300615 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300615 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300615/0 /scratch/stefan/7770550/working/building/REAL300000300615 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/894 `/scratch/stefan/7770550/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300615 none CSC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 33, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 33 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300615 none CSC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300615 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300615/1 /scratch/stefan/7770550/working/building/REAL300000300615 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/895 `/scratch/stefan/7770550/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300615.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300615 none CSC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 33, 17, 17, 1, 1, 1, 2, 2, 2, 17] 33 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 34, 33, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300615 none CSC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 5, 5, 5, 1, 1, 17, 17, 17, 17, 17, 17, 1] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300615 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300615 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300615/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300615/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300615 Building REAL300000300616 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300616' /scratch/stefan/7770550/working/building/REAL300000300616 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300616 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300616/0 /scratch/stefan/7770550/working/building/REAL300000300616 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/896 `/scratch/stefan/7770550/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300616 none CCC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 33, 33, 33, 33, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 33, 53, 53, 53, 53, 53, 33, 1, 1, 1, 2, 2, 2] 53 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 15, 16, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300616 none CCC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 33, 33, 17, 26, 33, 33, 33, 33, 33, 1, 8, 8, 8, 8, 8, 1, 33, 33, 33, 33, 33, 33] 53 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300616 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300616 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300616/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300616 Building REAL300000300617 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300617' /scratch/stefan/7770550/working/building/REAL300000300617 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300617 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300617/0 /scratch/stefan/7770550/working/building/REAL300000300617 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/897 `/scratch/stefan/7770550/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC2=NC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C12) `REAL300000300617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300617 none CCC1=NOC2=NC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 21, 21, 21, 21, 21, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 37, 37, 37, 37, 37, 21, 1, 1, 1, 2, 2, 2, 21] 37 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300617 none CCC1=NOC2=NC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 3, 3, 3, 3, 3, 1, 21, 21, 21, 21, 21, 21, 1] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 30, 37] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300617 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300617/1 /scratch/stefan/7770550/working/building/REAL300000300617 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/898 `/scratch/stefan/7770550/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC2=NC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C12) `REAL300000300617.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300617 none CCC1=NOC2=NC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 33, 33, 33, 33, 33, 17, 5, 1, 1, 1, 2, 2, 2, 17] 33 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300617 none CCC1=NOC2=NC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 3, 3, 3, 2, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 38, 30] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300617 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300617 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300617/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300617/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300617 Building REAL300000300618 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300618' /scratch/stefan/7770550/working/building/REAL300000300618 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300618 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300618/0 /scratch/stefan/7770550/working/building/REAL300000300618 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/899 `/scratch/stefan/7770550/working/3D/899' -> `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)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300618 none CC1=C([N+](=O)[O-])C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 35, 35, 35, 35, 35, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 32, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300618 none CC1=C([N+](=O)[O-])C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 23, 35, 35, 23, 31, 35, 35, 35, 35, 35, 1, 2, 2, 2, 1, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 22, 26] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300618 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300618 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300618/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300618 Building REAL300000300619 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300619' /scratch/stefan/7770550/working/building/REAL300000300619 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300619 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300619/0 /scratch/stefan/7770550/working/building/REAL300000300619 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/900 `/scratch/stefan/7770550/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN=C1Cl) `REAL300000300619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300619 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300619 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 19, 20, 21, 22, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300619 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300619/1 /scratch/stefan/7770550/working/building/REAL300000300619 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/901 `/scratch/stefan/7770550/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN=C1Cl) `REAL300000300619.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300619 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 7, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300619 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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: [3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 1, 1, 4, 4, 4, 1, 9, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 34, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300619 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300619 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300619/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300619/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300619 Building REAL300000300620 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300620' /scratch/stefan/7770550/working/building/REAL300000300620 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300620 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300620/0 /scratch/stefan/7770550/working/building/REAL300000300620 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/902 `/scratch/stefan/7770550/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(=O)OC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=CC=C21) `REAL300000300620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300620 none CCN1C(=O)OC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 33, 33, 33, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 33 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300620 none CCN1C(=O)OC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 16, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 23, 24, 25, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300620 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300620/1 /scratch/stefan/7770550/working/building/REAL300000300620 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/903 `/scratch/stefan/7770550/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(=O)OC2=CC(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)=CC=C21) `REAL300000300620.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300620 none CCN1C(=O)OC2=CC(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 33, 33, 33, 17, 1, 1, 1, 2, 2, 2, 17, 17] 33 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300620 none CCN1C(=O)OC2=CC(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 13, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 3, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 23, 24, 25, 38, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300620 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300620 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300620/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300620/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300620 Building REAL300000300621 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300621' /scratch/stefan/7770550/working/building/REAL300000300621 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300621 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300621/0 /scratch/stefan/7770550/working/building/REAL300000300621 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/904 `/scratch/stefan/7770550/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C3C(=C1)CC(=O)N3CCC2) `REAL300000300621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300621 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C3C(=C1)CC(=O)N3CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 12, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300621 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C3C(=C1)CC(=O)N3CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300621 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300621 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300621/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300621 Building REAL300000300622 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300622' /scratch/stefan/7770550/working/building/REAL300000300622 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300622 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300622/0 /scratch/stefan/7770550/working/building/REAL300000300622 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/905 `/scratch/stefan/7770550/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)N=C1) `REAL300000300622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300622 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300622 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300622 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300622/1 /scratch/stefan/7770550/working/building/REAL300000300622 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/906 `/scratch/stefan/7770550/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)N=C1) `REAL300000300622.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300622 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300622 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300622 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300622 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300622/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300622/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300622 Building REAL300000300623 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300623' /scratch/stefan/7770550/working/building/REAL300000300623 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300623 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300623/0 /scratch/stefan/7770550/working/building/REAL300000300623 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/907 `/scratch/stefan/7770550/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300623 none COC(=O)C1=CC(F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 17, 44, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 44, 44, 44, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 44 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300623 none COC(=O)C1=CC(F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 9, 9, 9, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 44 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 28, 29, 37] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300623 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300623/1 /scratch/stefan/7770550/working/building/REAL300000300623 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/908 `/scratch/stefan/7770550/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300623.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300623 none COC(=O)C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 17, 41, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 41, 41, 41, 17, 17, 1, 1, 1, 2, 2, 2, 17] 41 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300623 none COC(=O)C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 7, 7, 7, 1, 1, 17, 17, 17, 17, 17, 17, 1] 41 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 36, 28, 29] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300623 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300623 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300623/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300623/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300623 Building REAL300000300624 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300624' /scratch/stefan/7770550/working/building/REAL300000300624 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300624 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300624/0 /scratch/stefan/7770550/working/building/REAL300000300624 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/909 `/scratch/stefan/7770550/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(C)C(CC(=O)[O-])=C1C) `REAL300000300624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300624 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(C)C(CC(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 5, 1, 5, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 21, 23, 23, 23, 23, 17, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 23, 23, 23, 23, 23, 23, 17, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2] 35 rigid atoms, others: [37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 132 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300624 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(C)C(CC(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 5, 1, 5, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 23, 23, 23, 9, 11, 23, 23, 35, 35, 35, 23, 23, 2, 2, 2, 1, 1, 1, 5, 23, 23, 23, 23, 23, 23, 23, 35, 35, 23, 23, 23] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 229 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300624 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300624 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300624/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300624 Building REAL300000300625 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300625' /scratch/stefan/7770550/working/building/REAL300000300625 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300625 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300625/0 /scratch/stefan/7770550/working/building/REAL300000300625 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/910 `/scratch/stefan/7770550/working/3D/910' -> `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)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300625 none CC1=NN(CC(C)C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 39, 39, 39, 65, 65, 65, 39, 39, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 65, 65, 65, 65, 65, 65, 65, 65, 65, 39, 39, 39, 1, 1, 1, 2, 2, 2] 65 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300625 none CC1=NN(CC(C)C)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 5, 5, 1, 1, 1, 1, 10, 10, 10, 23, 39, 39, 23, 35, 39, 39, 39, 39, 39, 2, 2, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 39, 39, 39, 39, 39, 39] 65 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300625 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300625 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300625/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300625 Building REAL300000300626 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300626' /scratch/stefan/7770550/working/building/REAL300000300626 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300626 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300626/0 /scratch/stefan/7770550/working/building/REAL300000300626 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/911 `/scratch/stefan/7770550/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1F) `REAL300000300626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300626 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 1, 1, 1, 2, 2, 2, 29, 29, 29] 29 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300626 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 29, 29, 13, 19, 29, 29, 29, 29, 29, 1, 1, 1, 1, 3, 3, 3, 1, 1, 13, 29, 29, 29, 29, 29, 29, 2, 2, 2] 29 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300626 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300626 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300626/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300626 Building REAL300000300627 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300627' /scratch/stefan/7770550/working/building/REAL300000300627 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300627 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300627/0 /scratch/stefan/7770550/working/building/REAL300000300627 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/912 `/scratch/stefan/7770550/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1Cl) `REAL300000300627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300627 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 7, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300627 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300627 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300627/1 /scratch/stefan/7770550/working/building/REAL300000300627 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/913 `/scratch/stefan/7770550/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1Cl) `REAL300000300627.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300627 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 13, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1] 13 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300627 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300627 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300627 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300627/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300627/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300627 Building REAL300000300628 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300628' /scratch/stefan/7770550/working/building/REAL300000300628 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300628 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300628/0 /scratch/stefan/7770550/working/building/REAL300000300628 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/914 `/scratch/stefan/7770550/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2OC=CC2=CC=C1) `REAL300000300628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300628 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2OC=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 21, 21, 29, 29, 29, 29, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300628 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2OC=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', '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, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300628 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300628/1 /scratch/stefan/7770550/working/building/REAL300000300628 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/915 `/scratch/stefan/7770550/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2OC=CC2=CC=C1) `REAL300000300628.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300628 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2OC=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 20, 31, 31, 31, 31, 31, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 19, 1, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300628 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2OC=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 7, 31, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300628 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300628 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300628/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300628/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300628 Building REAL300000300629 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300629' /scratch/stefan/7770550/working/building/REAL300000300629 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300629 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300629/0 /scratch/stefan/7770550/working/building/REAL300000300629 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/916 `/scratch/stefan/7770550/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CN=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300629 none COC(=O)C1=CN=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 17, 39, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 39, 39, 39, 17, 17, 1, 1, 1, 2, 2, 2, 17] 39 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300629 none COC(=O)C1=CN=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 6, 6, 6, 1, 1, 17, 17, 17, 17, 17, 17, 1] 39 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 23, 27, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300629 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300629/1 /scratch/stefan/7770550/working/building/REAL300000300629 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/917 `/scratch/stefan/7770550/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CN=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300629.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300629 none COC(=O)C1=CN=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 17, 42, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 42, 42, 42, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 42 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300629 none COC(=O)C1=CN=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 9, 9, 9, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 42 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 36, 27, 28] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300629 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300629 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300629/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300629/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300629 Building REAL300000300630 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300630' /scratch/stefan/7770550/working/building/REAL300000300630 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300630 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300630/0 /scratch/stefan/7770550/working/building/REAL300000300630 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/918 `/scratch/stefan/7770550/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300630 none COCCOC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 179, 104, 39, 39, 39, 23, 39, 39, 39, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 179, 179, 39, 23, 39, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 721 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300630 none COCCOC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 49, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 39, 39, 19, 33, 39, 39, 39, 39, 39, 89, 89, 89, 49, 49, 32, 32, 1, 1, 1, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300630 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300630/1 /scratch/stefan/7770550/working/building/REAL300000300630 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/919 `/scratch/stefan/7770550/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300630.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300630 none COCCOC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 158, 93, 37, 37, 37, 21, 37, 37, 37, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 158, 158, 37, 21, 37, 5, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 39, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 767 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300630 none COCCOC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 40, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 37, 37, 21, 33, 37, 37, 37, 37, 37, 82, 82, 82, 40, 40, 21, 21, 1, 1, 1, 21, 37, 37, 37, 37, 37, 37] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300630 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300630 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300630/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300630/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300630 Building REAL300000300631 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300631' /scratch/stefan/7770550/working/building/REAL300000300631 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300631 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300631/0 /scratch/stefan/7770550/working/building/REAL300000300631 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/920 `/scratch/stefan/7770550/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)O1) `REAL300000300631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300631 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 17, 22, 22, 22, 22, 22, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 1, 1] 22 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300631 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 16, 16, 16, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 1, 22, 22] 22 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 23, 24, 25] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300631 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300631 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300631/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300631 Building REAL300000300632 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300632' /scratch/stefan/7770550/working/building/REAL300000300632 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300632 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300632/0 /scratch/stefan/7770550/working/building/REAL300000300632 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/921 `/scratch/stefan/7770550/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C2=CC=CC=C2)S1) `REAL300000300632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300632 none CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 18, 7, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 2, 2, 2, 74, 74, 74, 74, 74] 74 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300632 none CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 12, 12, 12, 34, 74, 74, 34, 73, 74, 74, 74, 74, 74, 1, 1, 4, 4, 1, 4, 4, 1, 2, 2, 2, 74, 74, 74, 74, 74, 74, 4, 4, 1, 4, 4] 74 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300632 none CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 17, 17, 17, 40, 74, 74, 40, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1] 74 rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 294 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300632 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300632 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300632/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300632 Building REAL300000300633 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300633' /scratch/stefan/7770550/working/building/REAL300000300633 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300633 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300633/0 /scratch/stefan/7770550/working/building/REAL300000300633 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/922 `/scratch/stefan/7770550/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C2=CC=CC=C2)O1) `REAL300000300633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300633 none CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 18, 8, 18, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 2, 2, 2, 85, 85, 85, 85, 85] 85 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300633 none CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 36, 85, 85, 36, 54, 85, 85, 85, 85, 85, 1, 1, 4, 4, 2, 4, 4, 1, 2, 2, 2, 85, 85, 85, 85, 85, 85, 4, 4, 2, 4, 4] 85 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300633 none CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 22, 22, 22, 53, 85, 85, 53, 68, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1] 85 rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 339 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300633 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300633 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300633/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300633 Building REAL300000300634 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300634' /scratch/stefan/7770550/working/building/REAL300000300634 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300634 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300634/0 /scratch/stefan/7770550/working/building/REAL300000300634 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/923 `/scratch/stefan/7770550/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1C) `REAL300000300634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300634 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 15, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 2, 2, 2, 1, 2, 2, 2] 19 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300634 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300634 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300634/1 /scratch/stefan/7770550/working/building/REAL300000300634 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/924 `/scratch/stefan/7770550/working/3D/924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1C) `REAL300000300634.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300634 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 17, 17, 26, 26, 26, 26, 17, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 1, 2, 2, 2, 1, 2, 2, 2] 26 rigid atoms, others: [35, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300634 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=C(C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 26, 26, 26, 26, 26, 22, 22, 26, 26, 26, 2, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300634 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300634 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300634/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300634/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300634 Building REAL300000300635 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300635' /scratch/stefan/7770550/working/building/REAL300000300635 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300635 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300635/0 /scratch/stefan/7770550/working/building/REAL300000300635 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/925 `/scratch/stefan/7770550/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC(C)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300635 none COC1=CC(C)=CC(C)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 8, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 2, 2, 2] 21 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 80 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300635 none COC1=CC(C)=CC(C)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 21, 21, 11, 11, 21, 21, 21, 21, 21, 4, 4, 4, 1, 2, 2, 2, 1, 2, 2, 2, 11, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 119 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300635 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300635/1 /scratch/stefan/7770550/working/building/REAL300000300635 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/926 `/scratch/stefan/7770550/working/3D/926' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300635.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300635 none COC1=CC(C)=CC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 18, 18, 18, 18, 18, 18, 18, 16, 8, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300635 none COC1=CC(C)=CC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 18, 18, 8, 8, 18, 18, 18, 18, 18, 4, 4, 4, 1, 2, 2, 2, 1, 2, 2, 2, 18, 18, 18, 18, 18, 18] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300635 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300635 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300635/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300635/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300635 Building REAL300000300636 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300636' /scratch/stefan/7770550/working/building/REAL300000300636 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300636 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300636/0 /scratch/stefan/7770550/working/building/REAL300000300636 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/927 `/scratch/stefan/7770550/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N(C)C)C=C1) `REAL300000300636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300636 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1] 17 rigid atoms, others: [38, 39, 11, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 44 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300636 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 17, 17, 17, 17, 17, 17, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300636 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300636 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300636/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300636 Building REAL300000300637 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300637' /scratch/stefan/7770550/working/building/REAL300000300637 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300637 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300637/0 /scratch/stefan/7770550/working/building/REAL300000300637 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/928 `/scratch/stefan/7770550/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300637 none CCOC(=O)C1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 90, 75, 19, 75, 19, 19, 19, 19, 19, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 94, 94, 94, 94, 94, 19, 19, 19, 19, 19, 8, 1, 1, 1, 2, 2, 2, 19] 94 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 274 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300637 none CCOC(=O)C1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [41, 29, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 19, 19, 5, 9, 19, 19, 19, 19, 19, 1, 41, 42, 42, 41, 41, 1, 1, 2, 2, 2, 5, 19, 19, 19, 19, 19, 19, 1] 94 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 43, 25, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 218 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300637 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300637/1 /scratch/stefan/7770550/working/building/REAL300000300637 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/929 `/scratch/stefan/7770550/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300637.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300637 none CCOC(=O)C1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 93, 81, 19, 81, 19, 19, 19, 19, 19, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 95, 95, 95, 95, 95, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19] 95 rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300637 none CCOC(=O)C1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [44, 26, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 7, 7, 19, 19, 19, 19, 19, 1, 44, 44, 44, 44, 44, 1, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19, 1] 95 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 25, 42, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300637 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300637 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300637/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300637/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300637 Building REAL300000300638 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300638' /scratch/stefan/7770550/working/building/REAL300000300638 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300638 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300638/0 /scratch/stefan/7770550/working/building/REAL300000300638 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/930 `/scratch/stefan/7770550/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(F)=C1Cl) `REAL300000300638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300638 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(F)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 15, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 7, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300638 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(F)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 15, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300638 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300638/1 /scratch/stefan/7770550/working/building/REAL300000300638 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/931 `/scratch/stefan/7770550/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(F)=C1Cl) `REAL300000300638.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300638 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(F)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 15, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 9, 13, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300638 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(F)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 15, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300638 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300638 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300638/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300638/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300638 Building REAL300000300639 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300639' /scratch/stefan/7770550/working/building/REAL300000300639 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300639 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300639/0 /scratch/stefan/7770550/working/building/REAL300000300639 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/932 `/scratch/stefan/7770550/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300639 none CC1=C(Cl)SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300639 none CC1=C(Cl)SC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 21, 21, 17, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300639 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300639 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300639/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300639 Building REAL300000300640 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300640' /scratch/stefan/7770550/working/building/REAL300000300640 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300640 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300640/0 /scratch/stefan/7770550/working/building/REAL300000300640 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/933 `/scratch/stefan/7770550/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(OC)=C1) `REAL300000300640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300640 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 46, 122, 46, 46, 46, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 46, 46, 59, 46, 122, 122, 122, 46, 46, 1, 1, 1, 2, 2, 2, 59, 59, 59, 46] 122 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300640 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 7, 23, 46, 46, 23, 23, 46, 46, 46, 46, 46, 1, 1, 3, 1, 12, 12, 12, 1, 1, 46, 46, 46, 46, 46, 46, 4, 4, 4, 1] 122 rigid atoms, others: [2, 4, 5, 6, 7, 8, 40, 22, 23, 25, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300640 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300640/1 /scratch/stefan/7770550/working/building/REAL300000300640 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/934 `/scratch/stefan/7770550/working/3D/934' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(OC)=C1) `REAL300000300640.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300640 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 33, 77, 27, 33, 33, 12, 5, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 37, 33, 77, 77, 77, 33, 33, 5, 1, 1, 1, 2, 2, 2, 37, 37, 37, 33] 77 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300640 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(OC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 7, 7, 7, 18, 33, 33, 28, 30, 33, 33, 33, 33, 33, 1, 1, 3, 1, 9, 9, 9, 1, 1, 18, 33, 33, 33, 33, 33, 33, 3, 3, 3, 1] 77 rigid atoms, others: [2, 4, 5, 6, 7, 8, 41, 22, 23, 25, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300640 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300640 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300640/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300640/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300640 Building REAL300000300641 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300641' /scratch/stefan/7770550/working/building/REAL300000300641 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300641 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300641/0 /scratch/stefan/7770550/working/building/REAL300000300641 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/935 `/scratch/stefan/7770550/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(F)F)=C1) `REAL300000300641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300641 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 8, 1] 33 rigid atoms, others: [32, 34, 11, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300641 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 9, 17, 17, 33, 33, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 9, 33, 17] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300641 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300641/1 /scratch/stefan/7770550/working/building/REAL300000300641 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/936 `/scratch/stefan/7770550/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(F)F)=C1) `REAL300000300641.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300641 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 15, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 7, 1] 33 rigid atoms, others: [33, 11, 14, 15, 16, 17, 18, 19, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 32]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300641 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 9, 17, 17, 33, 33, 17, 2, 2, 2, 1, 1, 1, 17, 17, 9, 33, 17] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300641 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300641 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300641/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300641/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300641 Building REAL300000300642 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300642' /scratch/stefan/7770550/working/building/REAL300000300642 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300642 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300642/0 /scratch/stefan/7770550/working/building/REAL300000300642 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/937 `/scratch/stefan/7770550/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C=C1F) `REAL300000300642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300642 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 19, 19, 26, 26, 26, 26, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1, 1] 26 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300642 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300642 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300642/1 /scratch/stefan/7770550/working/building/REAL300000300642 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/938 `/scratch/stefan/7770550/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1F) `REAL300000300642.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300642 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 22, 29, 29, 29, 29, 29, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1] 29 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300642 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 29, 29, 18, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300642 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300642 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300642/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300642/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300642 Building REAL300000300643 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300643' /scratch/stefan/7770550/working/building/REAL300000300643 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300643 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300643/0 /scratch/stefan/7770550/working/building/REAL300000300643 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/939 `/scratch/stefan/7770550/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300643 none CC1=CC(Br)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300643 none CC1=CC(Br)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300643 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300643/1 /scratch/stefan/7770550/working/building/REAL300000300643 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/940 `/scratch/stefan/7770550/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300643.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300643 none CC1=CC(Br)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300643 none CC1=CC(Br)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300643 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300643 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300643/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300643/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300643 Building REAL300000300644 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300644' /scratch/stefan/7770550/working/building/REAL300000300644 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300644 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300644/0 /scratch/stefan/7770550/working/building/REAL300000300644 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/941 `/scratch/stefan/7770550/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC(F)F)N=C1) `REAL300000300644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300644 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 15, 17, 25, 25, 25, 25, 9, 2, 1, 2, 2, 1, 1, 1, 1, 8, 23, 23, 1, 1, 25, 25, 25, 25, 25, 25, 1, 8, 8, 23, 1] 115 rigid atoms, others: [33, 11, 14, 15, 16, 17, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300644 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 25, 25, 25, 94, 115, 115, 25, 25, 2, 2, 2, 1, 1, 1, 25, 94, 94, 115, 25] 115 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300644 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300644 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300644/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300644 Building REAL300000300645 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300645' /scratch/stefan/7770550/working/building/REAL300000300645 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300645 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300645/0 /scratch/stefan/7770550/working/building/REAL300000300645 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/942 `/scratch/stefan/7770550/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300645 none CSC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 14, 14, 14, 14, 14, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 14, 14, 14, 14, 7, 1, 1, 1, 2, 2, 2] 22 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300645 none CSC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 14, 14, 6, 12, 14, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14] 22 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300645 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300645/1 /scratch/stefan/7770550/working/building/REAL300000300645 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/943 `/scratch/stefan/7770550/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300645.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300645 none CSC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 19, 19, 19, 19, 19, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 29, 29, 29, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2] 29 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300645 none CSC1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 19, 19, 11, 13, 19, 19, 19, 19, 19, 7, 7, 7, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19] 29 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300645 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300645 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300645/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300645/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300645 Building REAL300000300646 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300646' /scratch/stefan/7770550/working/building/REAL300000300646 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300646 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300646/0 /scratch/stefan/7770550/working/building/REAL300000300646 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/944 `/scratch/stefan/7770550/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1S(=O)(=O)N(C)C) `REAL300000300646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300646 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1S(=O)(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 7, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 15 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300646 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1S(=O)(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 15, 15, 13, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 13, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300646 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300646 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300646/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300646 Building REAL300000300647 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300647' /scratch/stefan/7770550/working/building/REAL300000300647 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300647 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300647/0 /scratch/stefan/7770550/working/building/REAL300000300647 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/945 `/scratch/stefan/7770550/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(=O)(=O)F)=C1) `REAL300000300647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300647 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(=O)(=O)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300647 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(S(=O)(=O)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 33, 33, 33, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 9, 17] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300647 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300647/1 /scratch/stefan/7770550/working/building/REAL300000300647 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/946 `/scratch/stefan/7770550/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(=O)(=O)F)=C1) `REAL300000300647.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300647 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(=O)(=O)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300647 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(S(=O)(=O)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 11, 11, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 9, 17, 17, 33, 33, 33, 17, 2, 2, 2, 1, 1, 1, 17, 17, 9, 17] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300647 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300647 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300647/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300647/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300647 Building REAL300000300648 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300648' /scratch/stefan/7770550/working/building/REAL300000300648 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300648 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300648/0 /scratch/stefan/7770550/working/building/REAL300000300648 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/947 `/scratch/stefan/7770550/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2=CC=CC=C2)N=C1) `REAL300000300648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300648 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 9, 9, 9, 9, 9, 9, 1, 3, 3, 2, 3, 3, 1] 17 rigid atoms, others: [32, 38, 11, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300648 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 9, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 9, 17, 17, 17, 17, 17, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300648 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 3, 1, 1, 1, 1, 1, 3] 17 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300648 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300648/1 /scratch/stefan/7770550/working/building/REAL300000300648 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/948 `/scratch/stefan/7770550/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C(C2=CC=CC=C2)N=C1) `REAL300000300648.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300648 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 2, 2, 1, 2, 2, 1] 17 rigid atoms, others: [33, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300648 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 16, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 17, 17, 9, 17, 17, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300648 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C(C2=CC=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 9, 2, 1, 1, 1, 1, 1, 2] 17 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39]) total number of confs: 86 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300648 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300648 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300648/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300648/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300648 Building REAL300000300649 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300649' /scratch/stefan/7770550/working/building/REAL300000300649 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300649 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300649/0 /scratch/stefan/7770550/working/building/REAL300000300649 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/949 `/scratch/stefan/7770550/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C(C)C) `REAL300000300649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300649 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2] 11 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300649 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300649 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300649 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300649/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300649 Building REAL300000300650 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300650' /scratch/stefan/7770550/working/building/REAL300000300650 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300650 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300650/0 /scratch/stefan/7770550/working/building/REAL300000300650 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/950 `/scratch/stefan/7770550/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(C)=CS1) `REAL300000300650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300650 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(C)=CS1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 40, 69, 40, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 69, 69, 69, 1, 1, 1, 2, 2, 2, 40, 40, 40, 40] 69 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 205 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300650 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(C)=CS1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 1, 11, 1, 1, 1, 11, 11, 11, 22, 40, 40, 36, 36, 40, 40, 40, 40, 40, 1, 1, 1, 1, 11, 11, 11, 40, 40, 40, 40, 40, 40, 2, 2, 2, 1] 69 rigid atoms, others: [2, 4, 5, 6, 20, 21, 22, 23, 36] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300650 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300650 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300650/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300650 Building REAL300000300651 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300651' /scratch/stefan/7770550/working/building/REAL300000300651 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300651 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300651/0 /scratch/stefan/7770550/working/building/REAL300000300651 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/951 `/scratch/stefan/7770550/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F) `REAL300000300651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300651 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 7, 1, 1, 1, 2, 2, 2, 23, 23] 23 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300651 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 9, 17, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 4, 4, 1, 9, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300651 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300651/1 /scratch/stefan/7770550/working/building/REAL300000300651 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/952 `/scratch/stefan/7770550/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1F) `REAL300000300651.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300651 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2, 23, 23] 23 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300651 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 9, 17, 23, 23, 23, 23, 23, 1, 1, 1, 1, 3, 3, 3, 1, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300651 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300651 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300651/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300651/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300651 Building REAL300000300652 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300652' /scratch/stefan/7770550/working/building/REAL300000300652 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300652 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300652/0 /scratch/stefan/7770550/working/building/REAL300000300652 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/953 `/scratch/stefan/7770550/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300652 none COC(=O)C1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 27, 41, 27, 27, 23, 27, 27, 27, 27, 27, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 41, 41, 41, 27, 27, 27, 1, 1, 1, 2, 2, 2] 41 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300652 none COC(=O)C1=CC=C([N+](=O)[O-])C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 7, 7, 7, 15, 27, 27, 15, 23, 27, 27, 27, 27, 27, 5, 5, 5, 1, 1, 1, 27, 27, 27, 27, 27, 27] 41 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 11, 12, 13, 30, 31] set([0, 1, 3, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300652 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300652 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300652/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300652 Building REAL300000300653 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300653' /scratch/stefan/7770550/working/building/REAL300000300653 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300653 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300653/0 /scratch/stefan/7770550/working/building/REAL300000300653 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/954 `/scratch/stefan/7770550/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2C(=C1)C=NN2C) `REAL300000300653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300653 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2C(=C1)C=NN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300653 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2C(=C1)C=NN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300653 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300653/1 /scratch/stefan/7770550/working/building/REAL300000300653 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/955 `/scratch/stefan/7770550/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2C(=C1)C=NN2C) `REAL300000300653.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300653 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2C(=C1)C=NN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300653 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2C(=C1)C=NN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300653 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300653 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300653/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300653/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300653 Building REAL300000300654 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300654' /scratch/stefan/7770550/working/building/REAL300000300654 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300654 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300654/0 /scratch/stefan/7770550/working/building/REAL300000300654 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/956 `/scratch/stefan/7770550/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC([N+](=O)[O-])=C1) `REAL300000300654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300654 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 13, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300654 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300654 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300654/1 /scratch/stefan/7770550/working/building/REAL300000300654 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/957 `/scratch/stefan/7770550/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC([N+](=O)[O-])=C1) `REAL300000300654.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300654 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 14, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300654 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300654 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300654 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300654/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300654/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300654 Building REAL300000300655 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300655' /scratch/stefan/7770550/working/building/REAL300000300655 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300655 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300655/0 /scratch/stefan/7770550/working/building/REAL300000300655 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/958 `/scratch/stefan/7770550/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2OCC1) `REAL300000300655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300655 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2OCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 29, 43, 45, 45, 45, 45, 29, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 198 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300655 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2OCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 2, 2, 2, 1, 1, 1, 7, 45, 45, 45, 45, 45, 45, 45, 45, 45] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300655 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300655 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300655/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300655 Building REAL300000300656 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300656' /scratch/stefan/7770550/working/building/REAL300000300656 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300656 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300656/0 /scratch/stefan/7770550/working/building/REAL300000300656 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/959 `/scratch/stefan/7770550/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300656 none COC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 55, 83, 19, 19, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 83, 83, 83, 55, 19, 19, 5, 1, 1, 1, 2, 2, 2, 19, 19] 83 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300656 none COC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 6, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 17, 17, 19, 19, 19, 19, 19, 1, 1, 10, 10, 10, 6, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 1] 83 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 23, 24, 38, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300656 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300656 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300656/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300656 Building REAL300000300657 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300657' /scratch/stefan/7770550/working/building/REAL300000300657 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300657 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300657/0 /scratch/stefan/7770550/working/building/REAL300000300657 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/960 `/scratch/stefan/7770550/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(C(F)(F)F)=C1) `REAL300000300657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300657 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300657 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300657 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300657/1 /scratch/stefan/7770550/working/building/REAL300000300657 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/961 `/scratch/stefan/7770550/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(C(F)(F)F)=C1) `REAL300000300657.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300657 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300657 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300657 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300657 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300657/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300657/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300657 Building REAL300000300658 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300658' /scratch/stefan/7770550/working/building/REAL300000300658 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300658 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300658/0 /scratch/stefan/7770550/working/building/REAL300000300658 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/962 `/scratch/stefan/7770550/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNS(=O)(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300658 none CCNS(=O)(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 33, 33, 33, 33, 33, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2] 33 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300658 none CCNS(=O)(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 27, 27, 9, 9, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27] 33 rigid atoms, others: [32, 33, 34, 3, 6, 7, 8, 9, 10, 11, 12, 35] set([0, 1, 2, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300658 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300658 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300658/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300658 Building REAL300000300659 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300659' /scratch/stefan/7770550/working/building/REAL300000300659 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300659 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300659/0 /scratch/stefan/7770550/working/building/REAL300000300659 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/963 `/scratch/stefan/7770550/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-]) `REAL300000300659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300659 none COC1=C(F)C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300659 none COC1=C(F)C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 3, 3, 3, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 29, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300659 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300659/1 /scratch/stefan/7770550/working/building/REAL300000300659 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/964 `/scratch/stefan/7770550/working/3D/964' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-]) `REAL300000300659.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300659 none COC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19] 19 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300659 none COC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 16, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 3, 3, 3, 1, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300659 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300659 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300659/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300659/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300659 Building REAL300000300660 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300660' /scratch/stefan/7770550/working/building/REAL300000300660 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300660 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300660/0 /scratch/stefan/7770550/working/building/REAL300000300660 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/965 `/scratch/stefan/7770550/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2CCCN12) `REAL300000300660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300660 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300660 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300660 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300660/1 /scratch/stefan/7770550/working/building/REAL300000300660 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/966 `/scratch/stefan/7770550/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2CCCN12) `REAL300000300660.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300660 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 19, 19, 23, 23, 23, 23, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 19, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300660 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2CCCN12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300660 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300660 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300660/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300660/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300660 Building REAL300000300661 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300661' /scratch/stefan/7770550/working/building/REAL300000300661 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300661 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300661/0 /scratch/stefan/7770550/working/building/REAL300000300661 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/967 `/scratch/stefan/7770550/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C#N)=CC=C1Cl) `REAL300000300661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300661 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C#N)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 11, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1, 1] 15 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300661 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C#N)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300661 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300661/1 /scratch/stefan/7770550/working/building/REAL300000300661 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/968 `/scratch/stefan/7770550/working/3D/968' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C#N)=CC=C1Cl) `REAL300000300661.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300661 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C#N)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 15, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1] 15 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300661 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C#N)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300661 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300661 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300661/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300661/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300661 Building REAL300000300662 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300662' /scratch/stefan/7770550/working/building/REAL300000300662 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300662 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300662/0 /scratch/stefan/7770550/working/building/REAL300000300662 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/969 `/scratch/stefan/7770550/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC(F)(F)F)N=C1) `REAL300000300662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300662 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 17, 17, 22, 22, 22, 22, 9, 3, 1, 3, 3, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 22, 22, 22, 22, 22, 22, 1, 9, 9, 1] 60 rigid atoms, others: [33, 11, 14, 15, 16, 17, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300662 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(CC(F)(F)F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 15, 15, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 7, 14, 14, 14, 22, 22, 22, 60, 60, 60, 60, 22, 22, 2, 2, 2, 1, 1, 1, 22, 60, 60, 22] 60 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300662 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300662 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300662/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300662 Building REAL300000300663 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300663' /scratch/stefan/7770550/working/building/REAL300000300663 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300663 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300663/0 /scratch/stefan/7770550/working/building/REAL300000300663 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/970 `/scratch/stefan/7770550/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300663 none CCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 19, 29, 29, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 25, 29, 29, 7, 1, 1, 1, 2, 2, 2] 29 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300663 none CCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 29, 29, 13, 21, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 1, 1, 1, 1, 13, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300663 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300663 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300663/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300663 Building REAL300000300664 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300664' /scratch/stefan/7770550/working/building/REAL300000300664 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300664 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300664/0 /scratch/stefan/7770550/working/building/REAL300000300664 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/971 `/scratch/stefan/7770550/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(OC)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300664 none COC1=CC=CC(OC)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 36, 36, 36, 19, 36, 36, 36, 49, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 49, 49, 49, 36, 19, 36, 49, 49, 49, 1, 1, 1, 2, 2, 2] 49 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300664 none COC1=CC=CC(OC)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 10, 10, 10, 20, 39, 39, 20, 28, 39, 39, 39, 39, 39, 4, 4, 4, 1, 1, 1, 4, 4, 4, 39, 39, 39, 39, 39, 39] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10, 27, 28, 29] set([0, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300664 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300664 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300664/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300664 Building REAL300000300665 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300665' /scratch/stefan/7770550/working/building/REAL300000300665 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300665 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300665/0 /scratch/stefan/7770550/working/building/REAL300000300665 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/972 `/scratch/stefan/7770550/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCCCCl) `REAL300000300665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300665 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCCCCl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 5, 5, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 55, 65, 103, 165, 2, 2, 2, 1, 1, 1, 7, 55, 55, 65, 65, 105, 105, 169, 169] 169 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 825 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300665 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300665 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300665/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300665 Building REAL300000300666 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300666' /scratch/stefan/7770550/working/building/REAL300000300666 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300666 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300666/0 /scratch/stefan/7770550/working/building/REAL300000300666 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/973 `/scratch/stefan/7770550/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC=C1F) `REAL300000300666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300666 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 23, 23, 33, 33, 33, 33, 23, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1] 33 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300666 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 33, 33, 33, 30, 33, 33, 33, 2, 2, 2, 1, 1, 1, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300666 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300666/1 /scratch/stefan/7770550/working/building/REAL300000300666 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/974 `/scratch/stefan/7770550/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=CC=C1F) `REAL300000300666.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300666 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 20, 28, 36, 36, 36, 36, 20, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 20, 2, 2, 2, 1, 1, 1] 36 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300666 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 36, 36, 36, 36, 36, 36, 36, 2, 2, 2, 1, 1, 1, 7, 36, 36, 36, 36, 36, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300666 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300666 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300666/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300666/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300666 Building REAL300000300667 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300667' /scratch/stefan/7770550/working/building/REAL300000300667 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300667 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300667/0 /scratch/stefan/7770550/working/building/REAL300000300667 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/975 `/scratch/stefan/7770550/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C=C1C) `REAL300000300667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300667 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300667 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300667 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300667 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300667/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300667 Building REAL300000300668 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300668' /scratch/stefan/7770550/working/building/REAL300000300668 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300668 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300668/0 /scratch/stefan/7770550/working/building/REAL300000300668 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/976 `/scratch/stefan/7770550/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC2=CC=CC(F)=C21) `REAL300000300668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300668 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC2=CC=CC(F)=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 13, 13, 29, 29, 29, 29, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300668 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC2=CC=CC(F)=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300668 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300668/1 /scratch/stefan/7770550/working/building/REAL300000300668 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/977 `/scratch/stefan/7770550/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC2=CC=CC(F)=C21) `REAL300000300668.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300668 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC2=CC=CC(F)=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 27, 27, 27, 27, 27, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300668 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC2=CC=CC(F)=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300668 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300668 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300668/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300668/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300668 Building REAL300000300669 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300669' /scratch/stefan/7770550/working/building/REAL300000300669 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300669 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300669/0 /scratch/stefan/7770550/working/building/REAL300000300669 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/978 `/scratch/stefan/7770550/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2CC2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300669 none CC1=NN(CC2CC2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 9, 1, 1, 1, 1, 23, 23, 23, 23, 79, 79, 79, 129, 175, 175, 130, 175, 175, 175, 175, 175, 175, 23, 23, 23, 9, 9, 1, 1, 1, 1, 1, 23, 23, 23, 175, 175, 175, 175, 175, 175] 175 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 30, 31] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 658 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300669 none CC1=NN(CC2CC2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 23, 23, 1, 1, 1, 1, 11, 11, 11, 24, 56, 56, 24, 37, 56, 56, 56, 56, 56, 2, 2, 2, 7, 7, 23, 23, 23, 23, 23, 2, 2, 2, 56, 56, 56, 56, 56, 56] 175 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 341 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300669 none CC1=NN(CC2CC2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [56, 56, 56, 56, 56, 129, 175, 175, 56, 56, 20, 7, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 129, 129, 175, 175, 175, 175, 175, 56, 56, 56, 1, 1, 1, 2, 2, 2] 175 rigid atoms, others: [38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 662 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300669 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300669 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300669/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300669 Building REAL300000300670 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300670' /scratch/stefan/7770550/working/building/REAL300000300670 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300670 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300670/0 /scratch/stefan/7770550/working/building/REAL300000300670 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/979 `/scratch/stefan/7770550/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)C=C1F) `REAL300000300670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300670 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 15, 19, 19, 19, 19, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300670 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300670 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300670/1 /scratch/stefan/7770550/working/building/REAL300000300670 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/980 `/scratch/stefan/7770550/working/3D/980' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C=C1F) `REAL300000300670.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300670 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300670 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300670 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300670 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300670/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300670/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300670 Building REAL300000300671 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300671' /scratch/stefan/7770550/working/building/REAL300000300671 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300671 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300671/0 /scratch/stefan/7770550/working/building/REAL300000300671 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/981 `/scratch/stefan/7770550/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C(C)C=CN=C12) `REAL300000300671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300671 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C(C)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 23, 27, 27, 27, 27, 27, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2, 1, 1] 27 rigid atoms, others: [32, 33, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300671 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C(C)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300671 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300671/1 /scratch/stefan/7770550/working/building/REAL300000300671 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/982 `/scratch/stefan/7770550/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C(C)C=CN=C12) `REAL300000300671.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300671 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C(C)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 15, 21, 25, 25, 25, 25, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 15, 1, 1, 1, 2, 2, 2, 1, 1] 25 rigid atoms, others: [32, 33, 34, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300671 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C(C)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300671 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300671 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300671/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300671/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300671 Building REAL300000300672 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300672' /scratch/stefan/7770550/working/building/REAL300000300672 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300672 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300672/0 /scratch/stefan/7770550/working/building/REAL300000300672 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/983 `/scratch/stefan/7770550/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(C(N)=O)=C1) `REAL300000300672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300672 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 2, 2, 1] 29 rigid atoms, others: [32, 35, 11, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300672 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC(C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 29, 29, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 29, 29, 17] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300672 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300672/1 /scratch/stefan/7770550/working/building/REAL300000300672 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/984 `/scratch/stefan/7770550/working/3D/984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(C(N)=O)=C1) `REAL300000300672.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300672 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 1] 19 rigid atoms, others: [34, 11, 14, 15, 16, 17, 18, 19, 20, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300672 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC(C(N)=O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 19, 19, 17, 2, 2, 2, 1, 1, 1, 17, 17, 19, 19, 17] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300672 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300672 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300672/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300672/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300672 Building REAL300000300673 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300673' /scratch/stefan/7770550/working/building/REAL300000300673 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300673 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300673/0 /scratch/stefan/7770550/working/building/REAL300000300673 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/985 `/scratch/stefan/7770550/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=NSN=C21) `REAL300000300673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300673 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=NSN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 17, 24, 26, 26, 26, 26, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 1, 1, 1] 26 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300673 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=NSN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300673 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300673/1 /scratch/stefan/7770550/working/building/REAL300000300673 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/986 `/scratch/stefan/7770550/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=NSN=C21) `REAL300000300673.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300673 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=NSN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 15, 27, 27, 27, 27, 27, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 15, 1, 1, 1] 27 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300673 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=NSN=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 14, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300673 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300673 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300673/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300673/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300673 Building REAL300000300674 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300674' /scratch/stefan/7770550/working/building/REAL300000300674 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300674 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300674/0 /scratch/stefan/7770550/working/building/REAL300000300674 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/987 `/scratch/stefan/7770550/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300674 none COC1=CN=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 20, 20, 20, 17, 17, 1, 1, 1, 2, 2, 2, 17] 20 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300674 none COC1=CN=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 20 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 33, 21, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300674 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300674/1 /scratch/stefan/7770550/working/building/REAL300000300674 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/988 `/scratch/stefan/7770550/working/3D/988' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300674.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300674 none COC1=CN=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 22, 22, 22, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 22 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300674 none COC1=CN=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 3, 3, 3, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 22 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 21, 25, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300674 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300674 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300674/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300674/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300674 Building REAL300000300675 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300675' /scratch/stefan/7770550/working/building/REAL300000300675 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300675 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300675/0 /scratch/stefan/7770550/working/building/REAL300000300675 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/989 `/scratch/stefan/7770550/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Br)=C1F) `REAL300000300675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300675 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Br)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 19, 19, 27, 27, 27, 27, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300675 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Br)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300675 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300675 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300675/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300675 Building REAL300000300676 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300676' /scratch/stefan/7770550/working/building/REAL300000300676 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300676 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300676/0 /scratch/stefan/7770550/working/building/REAL300000300676 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/990 `/scratch/stefan/7770550/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC) `REAL300000300676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300676 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 19, 91, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 39, 91, 91, 91, 19, 19, 7, 1, 1, 1, 2, 2, 2, 19, 39, 39, 39] 91 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300676 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 14, 17, 19, 19, 19, 19, 19, 1, 1, 1, 3, 9, 9, 9, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 3, 3, 3] 91 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 38, 29, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300676 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300676/1 /scratch/stefan/7770550/working/building/REAL300000300676 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/991 `/scratch/stefan/7770550/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1OC) `REAL300000300676.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300676 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 21, 67, 21, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 35, 67, 67, 67, 21, 21, 1, 1, 1, 2, 2, 2, 21, 35, 35, 35] 67 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300676 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 1, 3, 9, 9, 9, 1, 1, 21, 21, 21, 21, 21, 21, 1, 4, 4, 4] 67 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 29, 30, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300676 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300676 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300676/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300676/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300676 Building REAL300000300677 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300677' /scratch/stefan/7770550/working/building/REAL300000300677 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300677 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300677/0 /scratch/stefan/7770550/working/building/REAL300000300677 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/992 `/scratch/stefan/7770550/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCOCCS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300677 none COCCOCCOCCS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 191, 138, 76, 74, 32, 18, 17, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 76, 76, 74, 74, 18, 18, 17, 17, 5, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [40, 41, 42, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300677 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300677 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300677/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300677 Building REAL300000300678 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300678' /scratch/stefan/7770550/working/building/REAL300000300678 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300678 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300678/0 /scratch/stefan/7770550/working/building/REAL300000300678 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/993 `/scratch/stefan/7770550/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300678 none COC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [36, 34, 34, 34, 21, 34, 34, 43, 43, 43, 34, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 36, 36, 36, 34, 34, 43, 43, 43, 34, 1, 1, 1, 2, 2, 2] 43 rigid atoms, others: [35, 36, 37, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300678 none COC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7, 20, 34, 34, 20, 23, 34, 34, 34, 34, 34, 4, 4, 4, 1, 1, 3, 3, 3, 1, 34, 34, 34, 34, 34, 34] 43 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300678 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300678/1 /scratch/stefan/7770550/working/building/REAL300000300678 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/994 `/scratch/stefan/7770550/working/3D/994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300678.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300678 none COC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 17, 23, 23, 36, 36, 36, 23, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 36, 36, 36, 23, 5, 1, 1, 1, 2, 2, 2] 36 rigid atoms, others: [36, 37, 38, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300678 none COC1=CC=C(S(C)(=O)=O)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7, 13, 23, 23, 18, 21, 23, 23, 23, 23, 23, 4, 4, 4, 1, 1, 3, 3, 3, 1, 13, 23, 23, 23, 23, 23, 23] 36 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 34, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300678 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300678 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300678/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300678/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300678 Building REAL300000300679 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300679' /scratch/stefan/7770550/working/building/REAL300000300679 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300679 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300679/0 /scratch/stefan/7770550/working/building/REAL300000300679 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/995 `/scratch/stefan/7770550/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)OCO2) `REAL300000300679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300679 none CC1=CC2=C(C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 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, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2, 19, 19] 19 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300679 none CC1=CC2=C(C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 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, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 19, 19, 11, 14, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 1, 1, 11, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 27, 28, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300679 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300679 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300679/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300679 Building REAL300000300680 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300680' /scratch/stefan/7770550/working/building/REAL300000300680 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300680 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300680/0 /scratch/stefan/7770550/working/building/REAL300000300680 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/996 `/scratch/stefan/7770550/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300680 none COC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 23, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29, 29, 1, 1, 1, 2, 2, 2] 29 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300680 none COC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 17, 29, 29, 17, 17, 29, 29, 29, 29, 29, 3, 3, 3, 1, 1, 1, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [1, 2, 3, 4, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300680 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300680/1 /scratch/stefan/7770550/working/building/REAL300000300680 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/997 `/scratch/stefan/7770550/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300680.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300680 none COC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 7, 1, 1, 1, 2, 2, 2] 31 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300680 none COC1=C([N+](=O)[O-])C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 17, 31, 31, 20, 31, 31, 31, 31, 31, 31, 3, 3, 3, 1, 1, 1, 17, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [1, 2, 3, 4, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300680 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300680 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300680/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300680/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300680 Building REAL300000300681 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300681' /scratch/stefan/7770550/working/building/REAL300000300681 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300681 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300681/0 /scratch/stefan/7770550/working/building/REAL300000300681 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/998 `/scratch/stefan/7770550/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C(C)C(C(=O)[O-])=C1) `REAL300000300681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300681 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 5, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 5, 1, 2, 2, 2, 1] 9 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300681 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300681 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300681 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300681/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300681 Building REAL300000300682 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300682' /scratch/stefan/7770550/working/building/REAL300000300682 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300682 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300682/0 /scratch/stefan/7770550/working/building/REAL300000300682 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/999 `/scratch/stefan/7770550/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)N(C)C)C=C1) `REAL300000300682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300682 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1] 17 rigid atoms, others: [32, 33, 40, 41, 11, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300682 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 17, 17, 17, 17, 17, 17, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300682 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300682/1 /scratch/stefan/7770550/working/building/REAL300000300682 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1000 `/scratch/stefan/7770550/working/3D/1000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)N(C)C)C=C1) `REAL300000300682.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300682 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1] 17 rigid atoms, others: [32, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 35 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300682 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(=O)N(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 17, 17, 17, 17, 17, 17, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300682 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300682 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300682/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300682/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300682 Building REAL300000300683 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300683' /scratch/stefan/7770550/working/building/REAL300000300683 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300683 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300683/0 /scratch/stefan/7770550/working/building/REAL300000300683 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1001 `/scratch/stefan/7770550/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300683 none CCOC(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 70, 65, 37, 65, 37, 37, 25, 37, 37, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 78, 78, 78, 78, 78, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2] 78 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300683 none CCOC(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [29, 13, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 37, 37, 17, 27, 37, 37, 37, 37, 37, 29, 29, 29, 29, 29, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37] 78 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300683 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300683/1 /scratch/stefan/7770550/working/building/REAL300000300683 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1002 `/scratch/stefan/7770550/working/3D/1002' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300683.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300683 none CCOC(=O)C1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 93, 83, 27, 83, 27, 27, 19, 27, 27, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 27, 27, 27, 27, 7, 1, 1, 1, 2, 2, 2] 94 rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300683 none CCOC(=O)C1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [39, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 27, 27, 13, 17, 27, 27, 27, 27, 27, 39, 39, 39, 39, 39, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 27] 94 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300683 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300683 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300683/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300683/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300683 Building REAL300000300684 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300684' /scratch/stefan/7770550/working/building/REAL300000300684 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300684 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300684/0 /scratch/stefan/7770550/working/building/REAL300000300684 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1003 `/scratch/stefan/7770550/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300684 none CNS(=O)(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 2] 13 rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300684 none CNS(=O)(=O)C1=CC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 13, 13, 7, 7, 13, 13, 13, 13, 13, 3, 3, 3, 3, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [32, 2, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300684 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300684 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300684/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300684 Building REAL300000300685 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300685' /scratch/stefan/7770550/working/building/REAL300000300685 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300685 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300685/0 /scratch/stefan/7770550/working/building/REAL300000300685 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1004 `/scratch/stefan/7770550/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1Cl)CCC2=O) `REAL300000300685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300685 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1Cl)CCC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 8, 12, 16, 16, 16, 16, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300685 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1Cl)CCC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 1, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300685 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300685/1 /scratch/stefan/7770550/working/building/REAL300000300685 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1005 `/scratch/stefan/7770550/working/3D/1005' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1Cl)CCC2=O) `REAL300000300685.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300685 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1Cl)CCC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 7, 15, 15, 15, 15, 15, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300685 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C(C=C1Cl)CCC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300685 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300685 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300685/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300685/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300685 Building REAL300000300686 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300686' /scratch/stefan/7770550/working/building/REAL300000300686 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300686 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300686/0 /scratch/stefan/7770550/working/building/REAL300000300686 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1006 `/scratch/stefan/7770550/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300686 none CC(=O)NC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 37, 37, 37, 37, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 37, 51, 51, 51, 51, 37, 1, 1, 1, 2, 2, 2] 51 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300686 none CC(=O)NC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 37, 37, 23, 26, 37, 37, 37, 37, 37, 1, 5, 5, 5, 5, 1, 37, 37, 37, 37, 37, 37] 51 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300686 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300686/1 /scratch/stefan/7770550/working/building/REAL300000300686 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1007 `/scratch/stefan/7770550/working/3D/1007' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)[N-]C1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300686.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300686 none CC(=O)[N-]C1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 133, 146, 42, 42, 42, 42, 12, 5, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 42, 146, 146, 146, 42, 1, 1, 1, 2, 2, 2] 146 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 32, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300686 none CC(=O)[N-]C1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [47, 11, 47, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 42, 42, 20, 30, 42, 42, 42, 42, 42, 1, 47, 47, 47, 1, 42, 42, 42, 42, 42, 42] 146 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300686 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300686 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300686/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300686/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300686 Building REAL300000300687 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300687' /scratch/stefan/7770550/working/building/REAL300000300687 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300687 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300687/0 /scratch/stefan/7770550/working/building/REAL300000300687 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1008 `/scratch/stefan/7770550/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300687 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 45, 45, 45, 45, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 45 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300687 none CC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 6, 7, 7, 6, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 4, 4, 4, 4, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 45 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 24, 38, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300687 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300687/1 /scratch/stefan/7770550/working/building/REAL300000300687 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1009 `/scratch/stefan/7770550/working/3D/1009' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300687.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300687 none CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 45, 45, 45, 45, 17, 17, 1, 1, 1, 2, 2, 2, 17] 45 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300687 none CC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 4, 4, 4, 4, 1, 1, 17, 17, 17, 17, 17, 17, 1] 45 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 24, 29, 30, 37] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300687 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300687 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300687/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300687/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300687 Building REAL300000300688 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300688' /scratch/stefan/7770550/working/building/REAL300000300688 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300688 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300688/0 /scratch/stefan/7770550/working/building/REAL300000300688 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1010 `/scratch/stefan/7770550/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1OC) `REAL300000300688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300688 none COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 19, 19, 19, 19, 19, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 33, 33, 33, 33, 19, 1, 1, 1, 2, 2, 2, 19, 33, 33, 33] 33 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300688 none COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 19, 19, 9, 11, 19, 19, 19, 19, 19, 1, 1, 1, 4, 4, 4, 4, 1, 19, 19, 19, 19, 19, 19, 1, 4, 4, 4] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300688 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300688/1 /scratch/stefan/7770550/working/building/REAL300000300688 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1011 `/scratch/stefan/7770550/working/3D/1011' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC) `REAL300000300688.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300688 none COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 21, 21, 21, 21, 21, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 35, 35, 35, 35, 21, 7, 1, 1, 1, 2, 2, 2, 21, 35, 35, 35] 35 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300688 none COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 21, 21, 11, 15, 21, 21, 21, 21, 21, 1, 1, 1, 4, 4, 4, 4, 1, 11, 21, 21, 21, 21, 21, 21, 1, 4, 4, 4] 35 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300688 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300688 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300688/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300688/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300688 Building REAL300000300689 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300689' /scratch/stefan/7770550/working/building/REAL300000300689 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300689 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300689/0 /scratch/stefan/7770550/working/building/REAL300000300689 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1012 `/scratch/stefan/7770550/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)F)C(F)=C1) `REAL300000300689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300689 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 9, 17, 18, 18, 18, 18, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 10, 23, 23, 1, 1, 1, 18, 18, 18, 18, 18, 18, 9, 1, 1, 23, 1] 112 rigid atoms, others: [32, 33, 35, 11, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300689 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 10, 10, 10, 18, 18, 18, 18, 92, 112, 112, 18, 18, 18, 2, 2, 2, 1, 1, 1, 5, 18, 18, 112, 18] 112 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300689 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300689/1 /scratch/stefan/7770550/working/building/REAL300000300689 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1013 `/scratch/stefan/7770550/working/3D/1013' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OC(F)F)C(F)=C1) `REAL300000300689.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300689 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OC(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 9, 17, 21, 21, 21, 21, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 9, 24, 24, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 24, 1] 108 rigid atoms, others: [32, 34, 11, 14, 15, 16, 17, 18, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300689 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OC(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 91, 108, 108, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 108, 21] 108 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300689 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300689 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300689/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300689/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300689 Building REAL300000300690 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300690' /scratch/stefan/7770550/working/building/REAL300000300690 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300690 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300690/0 /scratch/stefan/7770550/working/building/REAL300000300690 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1014 `/scratch/stefan/7770550/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C(F)=C1) `REAL300000300690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300690 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300690 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300690 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300690/1 /scratch/stefan/7770550/working/building/REAL300000300690 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1015 `/scratch/stefan/7770550/working/3D/1015' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C(F)=C1) `REAL300000300690.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300690 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300690 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300690 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300690 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300690/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300690/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300690 Building REAL300000300691 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300691' /scratch/stefan/7770550/working/building/REAL300000300691 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300691 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300691/0 /scratch/stefan/7770550/working/building/REAL300000300691 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1016 `/scratch/stefan/7770550/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(C)(=O)=O)N=C1) `REAL300000300691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300691 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(C)(=O)=O)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 9, 17, 19, 19, 19, 19, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 5, 5, 5, 1] 35 rigid atoms, others: [35, 11, 14, 15, 16, 17, 18, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300691 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(S(C)(=O)=O)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 35, 35, 35, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 35, 35, 35, 19] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300691 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300691/1 /scratch/stefan/7770550/working/building/REAL300000300691 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1017 `/scratch/stefan/7770550/working/3D/1017' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(C)(=O)=O)N=C1) `REAL300000300691.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300691 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(C)(=O)=O)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 3, 3, 3, 1] 33 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300691 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(S(C)(=O)=O)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 33, 33, 33, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 33, 33, 33, 17] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300691 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300691 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300691/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300691/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300691 Building REAL300000300692 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300692' /scratch/stefan/7770550/working/building/REAL300000300692 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300692 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300692/0 /scratch/stefan/7770550/working/building/REAL300000300692 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1018 `/scratch/stefan/7770550/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1CC#N) `REAL300000300692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300692 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 13, 23, 35, 35, 35, 35, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 35, 35, 35, 35, 35, 13, 1, 1, 1, 1, 6, 6] 51 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300692 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC=C1CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 21, 21, 21, 35, 35, 21, 35, 35, 35, 51, 51, 2, 2, 2, 1, 1, 1, 8, 35, 35, 21, 35, 51, 51] 51 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300692 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300692/1 /scratch/stefan/7770550/working/building/REAL300000300692 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1019 `/scratch/stefan/7770550/working/3D/1019' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1CC#N) `REAL300000300692.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300692 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [42, 42, 42, 19, 19, 42, 42, 42, 42, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 6, 6] 55 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300692 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC=C1CC#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 42, 42, 19, 42, 42, 42, 55, 55, 2, 2, 2, 1, 1, 1, 42, 42, 28, 42, 55, 55] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300692 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300692 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300692/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300692/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300692 Building REAL300000300693 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300693' /scratch/stefan/7770550/working/building/REAL300000300693 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300693 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300693/0 /scratch/stefan/7770550/working/building/REAL300000300693 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1020 `/scratch/stefan/7770550/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300693 none CNS(=O)(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 17, 33, 33, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 33, 33, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 33 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300693 none CNS(=O)(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 3, 3, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 33 rigid atoms, others: [2, 5, 6, 7, 8, 9, 39, 23, 24, 25, 30, 31] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300693 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300693/1 /scratch/stefan/7770550/working/building/REAL300000300693 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1021 `/scratch/stefan/7770550/working/3D/1021' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300693.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300693 none CNS(=O)(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 17, 33, 33, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 33, 33, 33, 33, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 33 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300693 none CNS(=O)(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 3, 3, 1, 1, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 33 rigid atoms, others: [2, 5, 6, 7, 8, 9, 23, 24, 25, 38, 30, 31] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300693 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300693 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300693/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300693/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300693 Building REAL300000300694 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300694' /scratch/stefan/7770550/working/building/REAL300000300694 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300694 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300694/0 /scratch/stefan/7770550/working/building/REAL300000300694 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1022 `/scratch/stefan/7770550/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(CC#N)=C1) `REAL300000300694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300694 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(CC#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 8, 8, 1] 53 rigid atoms, others: [32, 35, 11, 14, 15, 16, 17, 18, 19, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300694 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(CC#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 9, 17, 17, 53, 53, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 9, 53, 53, 17] 53 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300694 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300694/1 /scratch/stefan/7770550/working/building/REAL300000300694 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1023 `/scratch/stefan/7770550/working/3D/1023' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(CC#N)=C1) `REAL300000300694.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300694 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(CC#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 11, 17, 22, 22, 22, 22, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 1, 22, 22, 22, 22, 22, 22, 1, 1, 1, 7, 7, 1] 50 rigid atoms, others: [34, 11, 14, 15, 16, 17, 18, 19, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300694 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(CC#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 14, 14, 14, 22, 22, 22, 22, 22, 50, 50, 22, 2, 2, 2, 1, 1, 1, 22, 22, 22, 50, 50, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300694 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300694 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300694/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300694/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300694 Building REAL300000300695 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300695' /scratch/stefan/7770550/working/building/REAL300000300695 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300695 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300695/0 /scratch/stefan/7770550/working/building/REAL300000300695 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1024 `/scratch/stefan/7770550/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C=C1Cl) `REAL300000300695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300695 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 7, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300695 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300695 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300695/1 /scratch/stefan/7770550/working/building/REAL300000300695 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1025 `/scratch/stefan/7770550/working/3D/1025' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1Cl) `REAL300000300695.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300695 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 13, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 7, 1, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300695 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 11, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300695 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300695 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300695/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300695/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300695 Building REAL300000300696 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300696' /scratch/stefan/7770550/working/building/REAL300000300696 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300696 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300696/0 /scratch/stefan/7770550/working/building/REAL300000300696 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1026 `/scratch/stefan/7770550/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(F)C=C1C) `REAL300000300696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300696 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 10, 12, 12, 12, 12, 12, 8, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 8, 2, 2, 2, 1, 1, 2, 2, 2] 12 rigid atoms, others: [33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300696 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 48 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300696 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300696 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300696/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300696 Building REAL300000300697 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300697' /scratch/stefan/7770550/working/building/REAL300000300697 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300697 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300697/0 /scratch/stefan/7770550/working/building/REAL300000300697 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1027 `/scratch/stefan/7770550/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(N)=NO1) `REAL300000300697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300697 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(N)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 37, 37] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300697 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(N)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 24, 37, 37, 24, 24, 37, 37, 37, 37, 37, 1, 1, 1, 1, 2, 2, 2, 37, 37, 37, 37, 37, 37, 1, 1] 37 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300697 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300697 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300697/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300697 Building REAL300000300698 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300698' /scratch/stefan/7770550/working/building/REAL300000300698 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300698 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300698/0 /scratch/stefan/7770550/working/building/REAL300000300698 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1028 `/scratch/stefan/7770550/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C)OCC(=O)N2) `REAL300000300698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300698 none COC1=CC2=C(C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C)OCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 2, 2, 2, 40, 40, 40] 40 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300698 none COC1=CC2=C(C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C)OCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 40, 40, 25, 25, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 40, 40, 40, 40, 40, 40, 1, 1, 1] 40 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 22, 23, 24, 25, 26, 38, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300698 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300698/1 /scratch/stefan/7770550/working/building/REAL300000300698 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1029 `/scratch/stefan/7770550/working/3D/1029' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=C(C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)OCC(=O)N2) `REAL300000300698.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300698 none COC1=CC2=C(C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)OCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 10, 6, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 2, 2, 2, 30, 30, 30] 30 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300698 none COC1=CC2=C(C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)OCC(=O)N2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 30, 30, 21, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 20, 30, 30, 30, 30, 30, 30, 1, 1, 1] 30 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 41, 39, 40, 22, 23, 24, 25, 26, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300698 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300698 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300698/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300698/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300698 Building REAL300000300699 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300699' /scratch/stefan/7770550/working/building/REAL300000300699 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300699 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300699/0 /scratch/stefan/7770550/working/building/REAL300000300699 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1030 `/scratch/stefan/7770550/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=C(F)C=C1Cl) `REAL300000300699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300699 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 12, 17, 17, 17, 17, 11, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300699 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300699 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300699/1 /scratch/stefan/7770550/working/building/REAL300000300699 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1031 `/scratch/stefan/7770550/working/3D/1031' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(Cl)C=C(F)C=C1Cl) `REAL300000300699.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300699 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(Cl)C=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 15, 17, 17, 17, 17, 11, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 11, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300699 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(Cl)C=C(F)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 15, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 8, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300699 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300699 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300699/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300699/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300699 Building REAL300000300700 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300700' /scratch/stefan/7770550/working/building/REAL300000300700 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300700 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300700/0 /scratch/stefan/7770550/working/building/REAL300000300700 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1032 `/scratch/stefan/7770550/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300700 none COC1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 43, 43, 43, 29, 43, 43, 43, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 47, 47, 47, 43, 35, 43, 1, 1, 1, 2, 2, 2] 47 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300700 none COC1=CC=C(Cl)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 43, 43, 25, 25, 43, 43, 43, 43, 43, 4, 4, 4, 1, 1, 1, 43, 43, 43, 43, 43, 43] 47 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300700 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300700/1 /scratch/stefan/7770550/working/building/REAL300000300700 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1033 `/scratch/stefan/7770550/working/3D/1033' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300700.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300700 none COC1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 13, 37, 37, 37, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 31, 37, 5, 1, 1, 1, 2, 2, 2] 37 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300700 none COC1=CC=C(Cl)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 37, 37, 21, 31, 37, 37, 37, 37, 37, 4, 4, 4, 1, 1, 1, 21, 37, 37, 37, 37, 37, 37] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300700 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300700 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300700/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300700/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300700 Building REAL300000300701 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300701' /scratch/stefan/7770550/working/building/REAL300000300701 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300701 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300701/0 /scratch/stefan/7770550/working/building/REAL300000300701 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1034 `/scratch/stefan/7770550/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC(C(F)(F)F)=C1) `REAL300000300701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300701 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300701 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300701 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300701/1 /scratch/stefan/7770550/working/building/REAL300000300701 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1035 `/scratch/stefan/7770550/working/3D/1035' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC(C(F)(F)F)=C1) `REAL300000300701.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300701 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300701 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300701 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300701 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300701/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300701/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300701 Building REAL300000300702 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300702' /scratch/stefan/7770550/working/building/REAL300000300702 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300702 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300702/0 /scratch/stefan/7770550/working/building/REAL300000300702 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1036 `/scratch/stefan/7770550/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300702 none COC1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 8, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 1, 1, 1, 2, 2, 2, 20] 20 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 80 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300702 none COC1=CC=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 20, 20, 5, 9, 20, 20, 20, 20, 20, 1, 3, 3, 3, 1, 1, 2, 2, 2, 5, 20, 20, 20, 20, 20, 20, 1] 20 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 38, 22, 26, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 118 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300702 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300702/1 /scratch/stefan/7770550/working/building/REAL300000300702 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1037 `/scratch/stefan/7770550/working/3D/1037' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300702.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300702 none COC1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19] 19 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300702 none COC1=CC=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 7, 7, 19, 19, 19, 19, 19, 1, 2, 2, 2, 1, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19, 1] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 26, 27, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300702 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300702 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300702/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300702/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300702 Building REAL300000300703 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300703' /scratch/stefan/7770550/working/building/REAL300000300703 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300703 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300703/0 /scratch/stefan/7770550/working/building/REAL300000300703 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1038 `/scratch/stefan/7770550/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C(Br)=C1) `REAL300000300703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300703 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300703 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300703 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300703/1 /scratch/stefan/7770550/working/building/REAL300000300703 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1039 `/scratch/stefan/7770550/working/3D/1039' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C(Br)=C1) `REAL300000300703.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300703 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300703 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300703 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300703 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300703/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300703/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300703 Building REAL300000300704 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300704' /scratch/stefan/7770550/working/building/REAL300000300704 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300704 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300704/0 /scratch/stefan/7770550/working/building/REAL300000300704 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1040 `/scratch/stefan/7770550/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300704 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 8, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300704 none COC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 21, 21, 5, 9, 21, 21, 21, 21, 21, 1, 1, 1, 3, 3, 3, 1, 2, 2, 2, 5, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 38, 21, 22, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300704 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300704 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300704/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300704 Building REAL300000300705 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300705' /scratch/stefan/7770550/working/building/REAL300000300705 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300705 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300705/0 /scratch/stefan/7770550/working/building/REAL300000300705 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1041 `/scratch/stefan/7770550/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=CC(Cl)=C1F) `REAL300000300705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300705 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 19, 19, 31, 31, 31, 31, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 1, 1] 31 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300705 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC([N+](=O)[O-])=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 11, 11, 1, 1, 16, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300705 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300705 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300705/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300705 Building REAL300000300706 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300706' /scratch/stefan/7770550/working/building/REAL300000300706 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300706 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300706/0 /scratch/stefan/7770550/working/building/REAL300000300706 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1042 `/scratch/stefan/7770550/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)S1) `REAL300000300706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300706 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 21, 21, 21, 21, 21, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300706 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300706 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300706 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300706/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300706 Building REAL300000300707 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300707' /scratch/stefan/7770550/working/building/REAL300000300707 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300707 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300707/0 /scratch/stefan/7770550/working/building/REAL300000300707 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1043 `/scratch/stefan/7770550/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=C([N+](=O)[O-])C=C1F) `REAL300000300707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300707 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 17, 17, 29, 29, 29, 29, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29, 29, 1, 1] 29 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300707 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 29, 29, 29, 19, 11, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300707 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300707 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300707/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300707 Building REAL300000300708 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300708' /scratch/stefan/7770550/working/building/REAL300000300708 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300708 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300708/0 /scratch/stefan/7770550/working/building/REAL300000300708 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1044 `/scratch/stefan/7770550/working/3D/1044' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300708 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300708 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300708 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300708/1 /scratch/stefan/7770550/working/building/REAL300000300708 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1045 `/scratch/stefan/7770550/working/3D/1045' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300708.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300708/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300708 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 14, 15, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300708 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 13, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300708 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300708 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300708/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300708/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300708 Building REAL300000300709 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300709' /scratch/stefan/7770550/working/building/REAL300000300709 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300709 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300709/0 /scratch/stefan/7770550/working/building/REAL300000300709 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1046 `/scratch/stefan/7770550/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2N=C1) `REAL300000300709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300709 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300709 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300709 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300709/1 /scratch/stefan/7770550/working/building/REAL300000300709 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1047 `/scratch/stefan/7770550/working/3D/1047' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2N=C1) `REAL300000300709.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300709 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300709 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300709 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300709 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300709/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300709/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300709 Building REAL300000300710 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300710' /scratch/stefan/7770550/working/building/REAL300000300710 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300710 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300710/0 /scratch/stefan/7770550/working/building/REAL300000300710 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1048 `/scratch/stefan/7770550/working/3D/1048' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-]) `REAL300000300710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300710 none COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 39, 39, 39, 39, 39, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 75, 75, 75, 75, 75, 39, 7, 1, 1, 1, 2, 2, 2, 39] 75 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 321 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300710 none COC1=CC(Cl)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 39, 39, 15, 27, 39, 39, 39, 39, 39, 1, 1, 1, 3, 3, 3, 3, 3, 1, 15, 39, 39, 39, 39, 39, 39, 1] 75 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 29, 37] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300710 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300710/1 /scratch/stefan/7770550/working/building/REAL300000300710 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1049 `/scratch/stefan/7770550/working/3D/1049' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-]) `REAL300000300710.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300710 none COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 38, 38, 38, 38, 38, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 38, 38, 38, 74, 74, 74, 74, 74, 38, 1, 1, 1, 2, 2, 2, 38] 74 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300710 none COC1=CC(Cl)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 38, 38, 15, 22, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 3, 3, 3, 1, 38, 38, 38, 38, 38, 38, 1] 74 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 36, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300710 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300710 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300710/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300710/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300710 Building REAL300000300711 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300711' /scratch/stefan/7770550/working/building/REAL300000300711 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300711 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300711/0 /scratch/stefan/7770550/working/building/REAL300000300711 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1050 `/scratch/stefan/7770550/working/3D/1050' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1) `REAL300000300711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300711 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 43, 65, 43, 43, 43, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 43, 43, 43, 65, 65, 65, 43, 43, 1, 1, 1, 2, 2, 2, 43] 65 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300711 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 7, 7, 7, 21, 43, 43, 21, 22, 43, 43, 43, 43, 43, 1, 1, 1, 11, 11, 11, 1, 1, 43, 43, 43, 43, 43, 43, 1] 65 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 36, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300711 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300711 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300711/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300711 Building REAL300000300712 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300712' /scratch/stefan/7770550/working/building/REAL300000300712 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300712 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300712/0 /scratch/stefan/7770550/working/building/REAL300000300712 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1051) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1051 `/scratch/stefan/7770550/working/3D/1051' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300712 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 17, 53, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 53, 53, 53, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 53 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300712 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 12, 12, 12, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 53 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 28, 29, 37] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300712 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300712/1 /scratch/stefan/7770550/working/building/REAL300000300712 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1052) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1052 `/scratch/stefan/7770550/working/3D/1052' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300712.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300712 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 17, 53, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 53, 53, 53, 17, 17, 1, 1, 1, 2, 2, 2, 17] 53 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300712 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 13, 13, 13, 1, 1, 17, 17, 17, 17, 17, 17, 1] 53 rigid atoms, others: [2, 4, 5, 6, 7, 8, 22, 23, 24, 36, 28, 29] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300712 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300712 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300712/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300712/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300712 Building REAL300000300713 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300713' /scratch/stefan/7770550/working/building/REAL300000300713 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300713 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300713/0 /scratch/stefan/7770550/working/building/REAL300000300713 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1053) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1053 `/scratch/stefan/7770550/working/3D/1053' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300713 none CCC(=O)C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 55, 25, 55, 25, 25, 25, 25, 25, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 59, 59, 59, 59, 59, 25, 25, 1, 1, 1, 2, 2, 2, 25] 59 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300713 none CCC(=O)C1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 25, 25, 11, 11, 25, 25, 25, 25, 25, 1, 36, 36, 36, 36, 36, 1, 1, 25, 25, 25, 25, 25, 25, 1] 59 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 38, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300713 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300713/1 /scratch/stefan/7770550/working/building/REAL300000300713 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1054) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1054 `/scratch/stefan/7770550/working/3D/1054' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300713.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300713 none CCC(=O)C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 78, 23, 78, 23, 23, 23, 23, 23, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 85, 85, 85, 85, 85, 23, 23, 7, 1, 1, 1, 2, 2, 2, 23] 85 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300713 none CCC(=O)C1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [35, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 23, 23, 9, 15, 23, 23, 23, 23, 23, 1, 35, 35, 35, 35, 35, 1, 1, 9, 23, 23, 23, 23, 23, 23, 1] 85 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 39, 24, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300713 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300713 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300713/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300713/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300713 Building REAL300000300714 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300714' /scratch/stefan/7770550/working/building/REAL300000300714 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300714 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300714/0 /scratch/stefan/7770550/working/building/REAL300000300714 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1055) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1055 `/scratch/stefan/7770550/working/3D/1055' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C#N) `REAL300000300714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300714 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300714 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300714 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300714/1 /scratch/stefan/7770550/working/building/REAL300000300714 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1056) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1056 `/scratch/stefan/7770550/working/3D/1056' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1C#N) `REAL300000300714.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300714 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300714 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 33, 34, 18, 19, 20, 21, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300714 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300714 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300714/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300714/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300714 Building REAL300000300715 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300715' /scratch/stefan/7770550/working/building/REAL300000300715 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300715 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300715/0 /scratch/stefan/7770550/working/building/REAL300000300715 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1057) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1057 `/scratch/stefan/7770550/working/3D/1057' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C(F)=C1) `REAL300000300715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300715 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300715 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300715 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300715/1 /scratch/stefan/7770550/working/building/REAL300000300715 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1058) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1058 `/scratch/stefan/7770550/working/3D/1058' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C(Cl)C(F)=C1) `REAL300000300715.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300715/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300715 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300715 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300715 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300715 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300715/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300715/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300715 Building REAL300000300716 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300716' /scratch/stefan/7770550/working/building/REAL300000300716 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300716 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300716/0 /scratch/stefan/7770550/working/building/REAL300000300716 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1059) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1059 `/scratch/stefan/7770550/working/3D/1059' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1) `REAL300000300716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300716 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 37] 37 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300716 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 37, 37, 19, 32, 37, 37, 37, 37, 37, 1, 1, 1, 3, 3, 3, 1, 1, 37, 37, 37, 37, 37, 37, 1] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300716 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300716/1 /scratch/stefan/7770550/working/building/REAL300000300716 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1060) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1060 `/scratch/stefan/7770550/working/3D/1060' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1) `REAL300000300716.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300716 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 23, 21, 37, 37, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 7, 1, 1, 1, 2, 2, 2, 37] 37 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300716 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 37, 37, 31, 33, 37, 37, 37, 37, 37, 1, 1, 1, 3, 3, 3, 1, 1, 21, 37, 37, 37, 37, 37, 37, 1] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300716 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300716 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300716/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300716/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300716 Building REAL300000300717 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300717' /scratch/stefan/7770550/working/building/REAL300000300717 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300717 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300717/0 /scratch/stefan/7770550/working/building/REAL300000300717 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1061) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1061 `/scratch/stefan/7770550/working/3D/1061' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC(C)=C1[N+](=O)[O-]) `REAL300000300717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300717 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC(C)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 5, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 2, 2, 2] 9 rigid atoms, others: [34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300717 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC(C)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 5, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300717 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300717 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300717/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300717 Building REAL300000300718 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300718' /scratch/stefan/7770550/working/building/REAL300000300718 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300718 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300718/0 /scratch/stefan/7770550/working/building/REAL300000300718 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1062) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1062 `/scratch/stefan/7770550/working/3D/1062' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC(F)(F)F)C=C1) `REAL300000300718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300718 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 7, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 5, 5, 1, 1] 23 rigid atoms, others: [32, 33, 36, 37, 11, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300718 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CC(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 23, 23, 9, 9] 23 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300718 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300718 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300718/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300718 Building REAL300000300719 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300719' /scratch/stefan/7770550/working/building/REAL300000300719 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300719 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300719/0 /scratch/stefan/7770550/working/building/REAL300000300719 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1063) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1063 `/scratch/stefan/7770550/working/3D/1063' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2OC1) `REAL300000300719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300719 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 43, 43, 28, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 28, 1, 1, 1, 1, 1, 1, 1] 43 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 117 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300719 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 20, 20, 20, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 1, 1, 1, 8, 43, 43, 43, 43, 43, 43, 43] 43 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300719 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300719 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300719/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300719 Building REAL300000300720 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300720' /scratch/stefan/7770550/working/building/REAL300000300720 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300720 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300720/0 /scratch/stefan/7770550/working/building/REAL300000300720 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1064) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1064 `/scratch/stefan/7770550/working/3D/1064' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1OC(F)(F)F) `REAL300000300720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300720 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1] 3 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 12 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300720 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300720 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300720 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300720/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300720 Building REAL300000300721 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300721' /scratch/stefan/7770550/working/building/REAL300000300721 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300721 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300721/0 /scratch/stefan/7770550/working/building/REAL300000300721 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1065) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1065 `/scratch/stefan/7770550/working/3D/1065' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)F)C=C1) `REAL300000300721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300721 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 5, 9, 12, 12, 12, 12, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 6, 6, 1, 1, 12, 12, 12, 12, 12, 12, 5, 1, 1, 6, 1, 1] 20 rigid atoms, others: [33, 34, 11, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300721 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 20, 20, 12, 12, 2, 2, 2, 1, 1, 1, 5, 12, 12, 20, 12, 12] 20 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300721 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300721 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300721/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300721 Building REAL300000300722 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300722' /scratch/stefan/7770550/working/building/REAL300000300722 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300722 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300722/0 /scratch/stefan/7770550/working/building/REAL300000300722 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1066) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1066 `/scratch/stefan/7770550/working/3D/1066' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C2=CC=CC=C2)=C1) `REAL300000300722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300722 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 9, 17, 25, 25, 25, 25, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 25, 25, 25, 25, 25, 25, 9, 1, 1, 1, 3, 3, 1, 3, 3, 1] 25 rigid atoms, others: [33, 34, 35, 41, 11, 14, 15, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300722 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300722 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 15, 25, 25, 25, 25, 25, 15, 5, 3, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 25, 25, 25, 25, 25, 25, 15, 3, 3, 3, 1, 1, 1, 1, 1, 3] 25 rigid atoms, others: [36, 37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 114 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300722 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300722/1 /scratch/stefan/7770550/working/building/REAL300000300722 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1067) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1067 `/scratch/stefan/7770550/working/3D/1067' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C2=CC=CC=C2)=C1) `REAL300000300722.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300722 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 10, 17, 26, 26, 26, 26, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 26, 26, 26, 26, 26, 26, 1, 1, 1, 3, 3, 1, 3, 3, 1] 26 rigid atoms, others: [32, 33, 34, 40, 11, 14, 15, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300722 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300722 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 24, 26, 26, 26, 26, 26, 16, 5, 3, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 26, 26, 26, 26, 26, 26, 3, 3, 3, 1, 1, 1, 1, 1, 3] 26 rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 61 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300722 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300722 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300722/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300722/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300722 Building REAL300000300723 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300723' /scratch/stefan/7770550/working/building/REAL300000300723 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300723 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300723/0 /scratch/stefan/7770550/working/building/REAL300000300723 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1068) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1068 `/scratch/stefan/7770550/working/3D/1068' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CN(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C1) `REAL300000300723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300723 none COC1CN(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 8, 1, 1, 1, 2, 2, 2, 29, 29] 29 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300723 none COC1CN(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 7, 7, 7, 19, 29, 29, 19, 25, 29, 29, 29, 29, 29, 1, 6, 6, 6, 1, 1, 1, 19, 29, 29, 29, 29, 29, 29, 1, 1] 29 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 19, 23, 24, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300723 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300723 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300723/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300723 Building REAL300000300724 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300724' /scratch/stefan/7770550/working/building/REAL300000300724 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300724 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300724/0 /scratch/stefan/7770550/working/building/REAL300000300724 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1069) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1069 `/scratch/stefan/7770550/working/3D/1069' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1) `REAL300000300724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300724 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 15, 6, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2, 27, 27, 27, 27] 27 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 32, 17, 18, 19, 20, 21, 22, 23, 33, 27, 28, 29, 30, 31]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300724 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 18, 27, 27, 18, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 2, 2, 2, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1] 27 rigid atoms, others: [0, 1, 2, 3, 33, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300724 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300724/1 /scratch/stefan/7770550/working/building/REAL300000300724 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1070) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1070 `/scratch/stefan/7770550/working/3D/1070' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1) `REAL300000300724.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300724 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 7, 1, 1, 1, 2, 2, 2, 24, 24, 24, 24] 24 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 78 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300724 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 16, 24, 24, 16, 16, 24, 24, 24, 24, 24, 1, 1, 1, 1, 2, 2, 2, 16, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1] 24 rigid atoms, others: [0, 1, 2, 3, 34, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300724 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300724 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300724/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300724/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300724 Building REAL300000300725 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300725' /scratch/stefan/7770550/working/building/REAL300000300725 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300725 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300725/0 /scratch/stefan/7770550/working/building/REAL300000300725 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1071) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1071 `/scratch/stefan/7770550/working/3D/1071' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300725 none CCOC(=O)C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 174, 162, 55, 162, 55, 55, 55, 55, 55, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 55, 177, 177, 177, 177, 177, 55, 55, 1, 1, 1, 2, 2, 2, 55] 177 rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300725 none CCOC(=O)C1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [61, 31, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 55, 55, 25, 31, 55, 55, 55, 55, 55, 1, 62, 62, 62, 61, 61, 1, 1, 55, 55, 55, 55, 55, 55, 1] 177 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 25, 39, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300725 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300725 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300725/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300725 Building REAL300000300726 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300726' /scratch/stefan/7770550/working/building/REAL300000300726 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300726 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300726/0 /scratch/stefan/7770550/working/building/REAL300000300726 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1072) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1072 `/scratch/stefan/7770550/working/3D/1072' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C) `REAL300000300726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300726 none CCOC(=O)C(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 193, 63, 193, 17, 63, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 201, 201, 201, 201, 201, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 201 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300726 none CCOC(=O)C(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 42, 40, 9, 40, 1, 9, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 64, 64, 64, 64, 64, 1, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 201 rigid atoms, others: [32, 5, 7, 8, 9, 10, 40, 24, 25, 26] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300726 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300726/1 /scratch/stefan/7770550/working/building/REAL300000300726 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1073) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1073 `/scratch/stefan/7770550/working/3D/1073' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C) `REAL300000300726.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300726 none CCOC(=O)C(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 193, 65, 193, 19, 65, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 201, 201, 201, 201, 201, 19, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19] 201 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 580 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300726 none CCOC(=O)C(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 44, 38, 11, 38, 1, 11, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 15, 19, 19, 19, 19, 19, 1, 1, 1, 62, 62, 62, 62, 62, 1, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2] 201 rigid atoms, others: [32, 5, 7, 8, 9, 10, 39, 24, 25, 26] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300726 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300726 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300726/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300726/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300726 Building REAL300000300727 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300727' /scratch/stefan/7770550/working/building/REAL300000300727 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300727 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300727/0 /scratch/stefan/7770550/working/building/REAL300000300727 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1074) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1074 `/scratch/stefan/7770550/working/3D/1074' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)O1) `REAL300000300727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300727 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 17, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300727 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.1', 'N.1', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300727 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300727 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300727/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300727 Building REAL300000300728 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300728' /scratch/stefan/7770550/working/building/REAL300000300728 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300728 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300728/0 /scratch/stefan/7770550/working/building/REAL300000300728 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1075) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1075 `/scratch/stefan/7770550/working/3D/1075' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C) `REAL300000300728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300728 none CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 170, 47, 170, 47, 47, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 47, 47, 47, 47, 47, 201, 201, 201, 201, 201, 47, 1, 1, 1, 2, 2, 2, 47, 47, 47, 47] 201 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300728 none CCOC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 27, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 23, 47, 47, 23, 23, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 1, 47, 47, 47, 47, 47, 47, 1, 2, 2, 2] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 39, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300728 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300728/1 /scratch/stefan/7770550/working/building/REAL300000300728 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1076) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1076 `/scratch/stefan/7770550/working/3D/1076' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C) `REAL300000300728.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300728 none CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 168, 47, 168, 47, 47, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 201, 201, 201, 201, 201, 47, 7, 1, 1, 1, 2, 2, 2, 47, 47, 47, 47] 201 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300728 none CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 24, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 23, 47, 47, 23, 41, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 1, 23, 47, 47, 47, 47, 47, 47, 1, 2, 2, 2] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 40, 22, 23, 24, 25, 26] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300728 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300728 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300728/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300728/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300728 Building REAL300000300729 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300729' /scratch/stefan/7770550/working/building/REAL300000300729 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300729 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300729/0 /scratch/stefan/7770550/working/building/REAL300000300729 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1077) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1077 `/scratch/stefan/7770550/working/3D/1077' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300729 none COCCNC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 152, 55, 55, 17, 55, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 195, 195, 195, 195, 195, 152, 152, 55, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 195 rigid atoms, others: [39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 870 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300729 none COCCNC(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [55, 49, 31, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 55, 55, 55, 49, 49, 31, 31, 5, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 195 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 45, 26, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300729 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300729/1 /scratch/stefan/7770550/working/building/REAL300000300729 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1078) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1078 `/scratch/stefan/7770550/working/3D/1078' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300729.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300729 none COCCNC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 95, 35, 35, 17, 35, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 136, 136, 136, 136, 136, 95, 95, 35, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 136 rigid atoms, others: [38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300729 none COCCNC(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [58, 39, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 16, 17, 17, 17, 17, 17, 17, 1, 58, 58, 58, 39, 39, 22, 22, 5, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1] 136 rigid atoms, others: [35, 36, 5, 7, 8, 9, 10, 11, 12, 44, 26, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300729 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300729 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300729/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300729/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300729 Building REAL300000300730 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300730' /scratch/stefan/7770550/working/building/REAL300000300730 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300730 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300730/0 /scratch/stefan/7770550/working/building/REAL300000300730 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1079) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1079 `/scratch/stefan/7770550/working/3D/1079' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300730 none COCC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 106, 45, 45, 25, 45, 45, 45, 71, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 45, 120, 120, 120, 106, 106, 45, 45, 71, 71, 71, 1, 1, 1, 2, 2, 2, 45] 120 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 549 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300730 none COCC1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 1, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 21, 45, 45, 21, 21, 45, 45, 45, 45, 45, 1, 20, 20, 20, 7, 7, 1, 1, 3, 3, 3, 45, 45, 45, 45, 45, 45, 1] 120 rigid atoms, others: [2, 3, 4, 5, 6, 7, 9, 10, 41, 24, 30, 31] set([0, 1, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300730 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300730/1 /scratch/stefan/7770550/working/building/REAL300000300730 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1080) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1080 `/scratch/stefan/7770550/working/3D/1080' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300730.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300730 none COCC1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 142, 48, 48, 23, 48, 48, 48, 65, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 148, 148, 148, 142, 142, 48, 48, 65, 65, 65, 7, 1, 1, 1, 2, 2, 2, 48] 148 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 638 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300730 none COCC1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [27, 9, 1, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 23, 48, 48, 23, 42, 48, 48, 48, 48, 48, 1, 27, 27, 27, 9, 9, 1, 1, 3, 3, 3, 23, 48, 48, 48, 48, 48, 48, 1] 148 rigid atoms, others: [2, 3, 4, 5, 6, 7, 9, 10, 24, 42, 30, 31] set([0, 1, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300730 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300730 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300730/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300730/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300730 Building REAL300000300731 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300731' /scratch/stefan/7770550/working/building/REAL300000300731 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300731 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300731/0 /scratch/stefan/7770550/working/building/REAL300000300731 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1081) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1081 `/scratch/stefan/7770550/working/3D/1081' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1) `REAL300000300731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300731 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 17, 17, 22, 22, 22, 22, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 9, 1, 1, 2, 2, 2, 1] 22 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300731 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 12, 12, 12, 22, 22, 12, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 1, 5, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300731 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300731 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300731/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300731 Building REAL300000300732 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300732' /scratch/stefan/7770550/working/building/REAL300000300732 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300732 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300732/0 /scratch/stefan/7770550/working/building/REAL300000300732 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1082) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1082 `/scratch/stefan/7770550/working/3D/1082' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300732 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300732 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 20, 21, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300732 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300732/1 /scratch/stefan/7770550/working/building/REAL300000300732 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1083) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1083 `/scratch/stefan/7770550/working/3D/1083' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1) `REAL300000300732.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300732 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300732 none COC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 20, 21, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300732 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300732 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300732/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300732/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300732 Building REAL300000300733 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300733' /scratch/stefan/7770550/working/building/REAL300000300733 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300733 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300733/0 /scratch/stefan/7770550/working/building/REAL300000300733 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1084) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1084 `/scratch/stefan/7770550/working/3D/1084' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1F) `REAL300000300733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300733 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 13, 14, 27, 27, 27, 27, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300733 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 19, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 11, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300733 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300733 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300733/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300733 Building REAL300000300734 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300734' /scratch/stefan/7770550/working/building/REAL300000300734 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300734 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300734/0 /scratch/stefan/7770550/working/building/REAL300000300734 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1085) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1085 `/scratch/stefan/7770550/working/3D/1085' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300734 none CCCC1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 24, 24, 18, 24, 24, 24, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 24, 61, 61, 61, 61, 61, 61, 61, 18, 24, 1, 1, 1, 2, 2, 2, 24] 61 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300734 none CCCC1=CC=C(Cl)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 24, 24, 10, 12, 24, 24, 24, 24, 24, 1, 16, 16, 16, 15, 15, 7, 7, 1, 1, 24, 24, 24, 24, 24, 24, 1] 61 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 39, 23, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300734 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300734/1 /scratch/stefan/7770550/working/building/REAL300000300734 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1086) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1086 `/scratch/stefan/7770550/working/3D/1086' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300734.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300734 none CCCC1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 25, 25, 17, 25, 25, 25, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 63, 63, 63, 63, 63, 63, 63, 19, 25, 7, 1, 1, 1, 2, 2, 2, 25] 63 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300734 none CCCC1=CC=C(Cl)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 25, 25, 11, 17, 25, 25, 25, 25, 25, 1, 16, 16, 16, 15, 15, 7, 7, 1, 1, 11, 25, 25, 25, 25, 25, 25, 1] 63 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 40, 23, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300734 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300734 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300734/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300734/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300734 Building REAL300000300735 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300735' /scratch/stefan/7770550/working/building/REAL300000300735 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300735 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300735/0 /scratch/stefan/7770550/working/building/REAL300000300735 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1087) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1087 `/scratch/stefan/7770550/working/3D/1087' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(C)C)=CC=C1Cl) `REAL300000300735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300735 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(C)C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 19, 9, 10, 19, 19, 19, 19, 9, 7, 1, 7, 7, 1, 1, 1, 1, 4, 4, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 4, 5, 5, 5, 5, 5, 5, 1, 1] 23 rigid atoms, others: [38, 39, 11, 14, 15, 16, 17, 20, 21, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300735 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(C)C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 19, 19, 19, 23, 23, 17, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 23, 23, 23, 23, 23, 23, 23, 19, 19] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300735 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300735/1 /scratch/stefan/7770550/working/building/REAL300000300735 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1088) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1088 `/scratch/stefan/7770550/working/3D/1088' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(C)C)=CC=C1Cl) `REAL300000300735.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300735 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(C)C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 19, 9, 13, 19, 19, 19, 19, 9, 7, 1, 7, 7, 1, 1, 1, 1, 4, 4, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 4, 5, 5, 5, 5, 5, 5, 1, 1] 23 rigid atoms, others: [39, 40, 11, 14, 15, 16, 17, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300735 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(C)C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 15, 15, 15, 19, 19, 19, 23, 23, 15, 19, 19, 19, 2, 2, 2, 1, 1, 1, 5, 19, 23, 23, 23, 23, 23, 23, 23, 17, 19] 23 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300735 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300735 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300735/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300735/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300735 Building REAL300000300736 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300736' /scratch/stefan/7770550/working/building/REAL300000300736 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300736 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300736/0 /scratch/stefan/7770550/working/building/REAL300000300736 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1089) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1089 `/scratch/stefan/7770550/working/3D/1089' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1C(F)(F)F) `REAL300000300736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300736 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 5, 5, 12, 12, 12, 12, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 1, 1, 1] 12 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300736 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300736 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300736/1 /scratch/stefan/7770550/working/building/REAL300000300736 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1090) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1090 `/scratch/stefan/7770550/working/3D/1090' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC=C1C(F)(F)F) `REAL300000300736.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300736 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300736 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300736 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300736 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300736/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300736/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300736 Building REAL300000300737 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300737' /scratch/stefan/7770550/working/building/REAL300000300737 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300737 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300737/0 /scratch/stefan/7770550/working/building/REAL300000300737 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1091) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1091 `/scratch/stefan/7770550/working/3D/1091' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC2=CC=CC=C12) `REAL300000300737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300737 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', '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, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 19, 29, 31, 31, 31, 31, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300737 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', '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, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 31, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300737 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300737/1 /scratch/stefan/7770550/working/building/REAL300000300737 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1092) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1092 `/scratch/stefan/7770550/working/3D/1092' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC2=CC=CC=C12) `REAL300000300737.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300737 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 19, 31, 31, 31, 31, 31, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 19, 1, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300737 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 7, 31, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300737 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300737 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300737/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300737/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300737 Building REAL300000300738 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300738' /scratch/stefan/7770550/working/building/REAL300000300738 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300738 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300738/0 /scratch/stefan/7770550/working/building/REAL300000300738 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1093) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1093 `/scratch/stefan/7770550/working/3D/1093' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300738 none CCOC(=O)CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 58, 201, 17, 17, 9, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 201, 201, 201, 201, 201, 58, 58, 9, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 201 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 634 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300738 none CCOC(=O)CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 44, 42, 7, 42, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 63, 63, 63, 63, 63, 7, 7, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 43, 25] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300738 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300738 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300738/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300738 Building REAL300000300739 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300739' /scratch/stefan/7770550/working/building/REAL300000300739 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300739 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300739/0 /scratch/stefan/7770550/working/building/REAL300000300739 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1094) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1094 `/scratch/stefan/7770550/working/3D/1094' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1) `REAL300000300739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300739 none CCOC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 82, 80, 27, 80, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 85, 85, 85, 85, 85, 1, 1, 1, 2, 2, 2, 27, 27, 27, 27] 85 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 239 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300739 none CCOC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 14, 12, 1, 12, 1, 1, 1, 9, 9, 9, 13, 27, 27, 13, 21, 27, 27, 27, 27, 27, 1, 1, 1, 1, 25, 25, 25, 25, 25, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1] 85 rigid atoms, others: [3, 5, 6, 7, 39, 21, 22, 23, 24] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300739 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300739 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300739/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300739 Building REAL300000300740 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300740' /scratch/stefan/7770550/working/building/REAL300000300740 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300740 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300740/0 /scratch/stefan/7770550/working/building/REAL300000300740 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1095) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1095 `/scratch/stefan/7770550/working/3D/1095' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300740 none CCOC(=O)C1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 153, 46, 153, 46, 46, 46, 46, 46, 70, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 46, 201, 201, 201, 201, 201, 46, 46, 70, 70, 70, 1, 1, 1, 2, 2, 2, 46] 201 rigid atoms, others: [37, 38, 39, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 619 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300740 none CCOC(=O)C1=CC=C(OC)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 14, 10, 1, 10, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 25, 46, 46, 25, 25, 46, 46, 46, 46, 46, 1, 37, 37, 37, 36, 36, 1, 1, 3, 3, 3, 46, 46, 46, 46, 46, 46, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 11, 12, 43, 26] set([0, 1, 2, 4, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300740 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300740/1 /scratch/stefan/7770550/working/building/REAL300000300740 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1096) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1096 `/scratch/stefan/7770550/working/3D/1096' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300740.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300740 none CCOC(=O)C1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 178, 164, 41, 164, 41, 41, 41, 41, 41, 43, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 183, 183, 183, 183, 183, 41, 41, 43, 43, 43, 5, 1, 1, 1, 2, 2, 2, 41] 183 rigid atoms, others: [38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 461 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300740 none CCOC(=O)C1=CC=C(OC)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [31, 17, 11, 1, 11, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 23, 41, 41, 38, 39, 41, 41, 41, 41, 41, 1, 31, 31, 31, 31, 31, 1, 1, 4, 4, 4, 23, 41, 41, 41, 41, 41, 41, 1] 183 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 11, 12, 44, 26] set([0, 1, 2, 4, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300740 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300740 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300740/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300740/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300740 Building REAL300000300741 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300741' /scratch/stefan/7770550/working/building/REAL300000300741 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300741 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300741/0 /scratch/stefan/7770550/working/building/REAL300000300741 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1097) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1097 `/scratch/stefan/7770550/working/3D/1097' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C) `REAL300000300741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300741 none CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 116, 27, 116, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 154, 154, 154, 154, 154, 27, 7, 1, 1, 1, 2, 2, 2, 27, 27, 27, 27, 27] 154 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300741 none CCOC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [33, 25, 9, 1, 9, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 9, 17, 27, 27, 27, 27, 27, 1, 1, 1, 1, 33, 33, 33, 33, 33, 1, 9, 27, 27, 27, 27, 27, 27, 1, 1, 2, 2, 2] 154 rigid atoms, others: [3, 5, 6, 7, 8, 39, 40, 22, 23, 24, 25, 31] set([0, 1, 2, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300741 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300741 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300741/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300741 Building REAL300000300742 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300742' /scratch/stefan/7770550/working/building/REAL300000300742 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300742 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300742/0 /scratch/stefan/7770550/working/building/REAL300000300742 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1098) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1098 `/scratch/stefan/7770550/working/3D/1098' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OC(C)(C)C2) `REAL300000300742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300742 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 27, 33, 33, 33, 33, 33, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 33 rigid atoms, others: [32, 33, 40, 41, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300742 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 16, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300742 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300742/1 /scratch/stefan/7770550/working/building/REAL300000300742 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1099) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1099 `/scratch/stefan/7770550/working/3D/1099' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OC(C)(C)C2) `REAL300000300742.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300742 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 19, 29, 34, 34, 34, 34, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 19, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 34 rigid atoms, others: [32, 33, 34, 41, 42, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300742 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OC(C)(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 2, 2, 2, 1, 1, 1, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300742 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300742 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300742/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300742/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300742 Building REAL300000300743 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300743' /scratch/stefan/7770550/working/building/REAL300000300743 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300743 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300743/0 /scratch/stefan/7770550/working/building/REAL300000300743 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1100) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1100 `/scratch/stefan/7770550/working/3D/1100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C(C#N)=C1) `REAL300000300743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300743 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300743 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300743 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300743/1 /scratch/stefan/7770550/working/building/REAL300000300743 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1101) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1101 `/scratch/stefan/7770550/working/3D/1101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C(C#N)=C1) `REAL300000300743.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300743 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300743 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300743 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300743 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300743/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300743/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300743 Building REAL300000300744 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300744' /scratch/stefan/7770550/working/building/REAL300000300744 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300744 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300744/0 /scratch/stefan/7770550/working/building/REAL300000300744 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1102) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1102 `/scratch/stefan/7770550/working/3D/1102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCO2) `REAL300000300744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300744 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 20, 28, 28, 28, 28, 28, 20, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1] 28 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300744 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 1, 1, 1, 28, 28, 28, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300744 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300744/1 /scratch/stefan/7770550/working/building/REAL300000300744 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1103) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1103 `/scratch/stefan/7770550/working/3D/1103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCO2) `REAL300000300744.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300744 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 20, 20, 27, 27, 27, 27, 20, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 20, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300744 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300744 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300744 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300744/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300744/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300744 Building REAL300000300745 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300745' /scratch/stefan/7770550/working/building/REAL300000300745 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300745 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300745/0 /scratch/stefan/7770550/working/building/REAL300000300745 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1104) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1104 `/scratch/stefan/7770550/working/3D/1104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Br)=C1C#N) `REAL300000300745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300745 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Br)=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 10, 10, 18, 18, 18, 18, 10, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 1, 1, 1] 18 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300745 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(Br)=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1, 1, 1, 18, 18, 18] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300745 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300745/1 /scratch/stefan/7770550/working/building/REAL300000300745 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1105) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1105 `/scratch/stefan/7770550/working/3D/1105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Br)=C1C#N) `REAL300000300745.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300745 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Br)=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 8, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300745 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(Br)=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 17, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 14, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 8, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300745 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300745 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300745/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300745/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300745 Building REAL300000300746 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300746' /scratch/stefan/7770550/working/building/REAL300000300746 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300746 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300746/0 /scratch/stefan/7770550/working/building/REAL300000300746 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1106) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1106 `/scratch/stefan/7770550/working/3D/1106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1C) `REAL300000300746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300746 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 15, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300746 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 13, 13, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300746 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300746 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300746/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300746 Building REAL300000300747 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300747' /scratch/stefan/7770550/working/building/REAL300000300747 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300747 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300747/0 /scratch/stefan/7770550/working/building/REAL300000300747 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1107) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1107 `/scratch/stefan/7770550/working/3D/1107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300747 none CCOC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 21, 21, 21, 21, 21, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 51, 51, 51, 51, 51, 21, 21, 21, 5, 1, 1, 1, 2, 2, 2, 21] 51 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 113 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300747 none CCOC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 13, 13, 13, 13, 13, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1] 51 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 22, 38, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 146 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300747 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300747/1 /scratch/stefan/7770550/working/building/REAL300000300747 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1108) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1108 `/scratch/stefan/7770550/working/3D/1108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300747.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300747 none CCOC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 21, 21, 21, 21, 21, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 43, 43, 43, 43, 43, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21] 43 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300747 none CCOC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 21, 21, 11, 17, 21, 21, 21, 21, 21, 1, 13, 13, 13, 13, 13, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1] 43 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 22, 28, 29, 30, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300747 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300747 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300747/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300747/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300747 Building REAL300000300748 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300748' /scratch/stefan/7770550/working/building/REAL300000300748 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300748 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300748/0 /scratch/stefan/7770550/working/building/REAL300000300748 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1109) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1109 `/scratch/stefan/7770550/working/3D/1109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC(F)=C1F) `REAL300000300748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300748 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 18, 18, 31, 31, 31, 31, 18, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 1, 1] 31 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300748 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300748 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300748 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300748/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300748 Building REAL300000300749 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300749' /scratch/stefan/7770550/working/building/REAL300000300749 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300749 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300749/0 /scratch/stefan/7770550/working/building/REAL300000300749 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1110) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1110 `/scratch/stefan/7770550/working/3D/1110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2C=C1) `REAL300000300749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300749 none CC1=CC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17] 17 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300749 none CC1=CC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 39, 21, 22, 23, 24, 38, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300749 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300749/1 /scratch/stefan/7770550/working/building/REAL300000300749 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1111) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1111 `/scratch/stefan/7770550/working/3D/1111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2C=C1) `REAL300000300749.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300749 none CC1=CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17, 17] 17 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300749 none CC1=CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 21, 22, 23, 24, 38, 28, 29, 30, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300749 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300749 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300749/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300749/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300749 Building REAL300000300750 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300750' /scratch/stefan/7770550/working/building/REAL300000300750 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300750 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300750/0 /scratch/stefan/7770550/working/building/REAL300000300750 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1112) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1112 `/scratch/stefan/7770550/working/3D/1112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CS1) `REAL300000300750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300750 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 32, 32, 44, 44, 44, 44, 32, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 1, 1] 44 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 174 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300750 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 44, 44, 44, 44, 44, 2, 2, 2, 1, 1, 1, 44, 44] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300750 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300750 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300750/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300750 Building REAL300000300751 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300751' /scratch/stefan/7770550/working/building/REAL300000300751 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300751 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300751/0 /scratch/stefan/7770550/working/building/REAL300000300751 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1113) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1113 `/scratch/stefan/7770550/working/3D/1113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(Cl)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300751 none COC(=O)C1=CC(Cl)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 37, 17, 17, 17, 17, 17, 17, 17, 8, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 37, 37, 37, 17, 17, 17, 17, 8, 1, 1, 1, 2, 2, 2, 17] 37 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300751 none COC(=O)C1=CC(Cl)=C(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 17, 17, 5, 9, 17, 17, 17, 17, 17, 1, 7, 7, 7, 1, 2, 2, 2, 5, 17, 17, 17, 17, 17, 17, 1] 37 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 40, 25, 29] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300751 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300751/1 /scratch/stefan/7770550/working/building/REAL300000300751 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1114) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1114 `/scratch/stefan/7770550/working/3D/1114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(Cl)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300751.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300751 none COC(=O)C1=CC(Cl)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 15, 33, 15, 15, 15, 15, 15, 15, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 33, 33, 33, 15, 15, 15, 15, 1, 1, 1, 2, 2, 2, 15] 33 rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300751 none COC(=O)C1=CC(Cl)=C(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 16, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 15, 15, 5, 5, 15, 15, 15, 15, 15, 1, 8, 8, 8, 1, 2, 2, 2, 15, 15, 15, 15, 15, 15, 1] 33 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 25, 29, 39] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300751 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300751 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300751/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300751/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300751 Building REAL300000300752 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300752' /scratch/stefan/7770550/working/building/REAL300000300752 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300752 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300752/0 /scratch/stefan/7770550/working/building/REAL300000300752 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1115) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1115 `/scratch/stefan/7770550/working/3D/1115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300752 none CC1=CSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300752 none CC1=CSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 17, 21, 21, 17, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 1, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300752 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300752 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300752/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300752 Building REAL300000300753 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300753' /scratch/stefan/7770550/working/building/REAL300000300753 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300753 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300753/0 /scratch/stefan/7770550/working/building/REAL300000300753 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1116) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1116 `/scratch/stefan/7770550/working/3D/1116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(NC(=O)C(C)C)C=C1) `REAL300000300753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300753 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(NC(=O)C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 5, 9, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 24, 24, 1, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 11, 24, 24, 24, 24, 24, 24, 24, 1, 1] 86 rigid atoms, others: [33, 34, 43, 44, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300753 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(NC(=O)C(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 66, 66, 66, 86, 86, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 66, 86, 86, 86, 86, 86, 86, 86, 15, 15] 86 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300753 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300753 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300753/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300753 Building REAL300000300754 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300754' /scratch/stefan/7770550/working/building/REAL300000300754 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300754 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300754/0 /scratch/stefan/7770550/working/building/REAL300000300754 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1117) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1117 `/scratch/stefan/7770550/working/3D/1117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNN=C1Cl) `REAL300000300754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300754 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 13, 19, 19, 19, 19, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300754 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300754 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300754 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300754/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300754 Building REAL300000300755 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300755' /scratch/stefan/7770550/working/building/REAL300000300755 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300755 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300755/0 /scratch/stefan/7770550/working/building/REAL300000300755 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1118) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1118 `/scratch/stefan/7770550/working/3D/1118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C(Cl)C=CN=C12) `REAL300000300755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300755 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C(Cl)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 15, 27, 27, 27, 27, 27, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300755 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C(Cl)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300755 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300755/1 /scratch/stefan/7770550/working/building/REAL300000300755 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1119) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1119 `/scratch/stefan/7770550/working/3D/1119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C(Cl)C=CN=C12) `REAL300000300755.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300755 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C(Cl)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 15, 15, 26, 26, 26, 26, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 15, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300755 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C(Cl)C=CN=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 7, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300755 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300755 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300755/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300755/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300755 Building REAL300000300756 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300756' /scratch/stefan/7770550/working/building/REAL300000300756 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300756 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300756/0 /scratch/stefan/7770550/working/building/REAL300000300756 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1120) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1120 `/scratch/stefan/7770550/working/3D/1120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)N=C1F) `REAL300000300756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300756 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)N=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 15, 15, 15, 15, 15, 7, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1] 15 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300756 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)N=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300756 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300756 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300756/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300756 Building REAL300000300757 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300757' /scratch/stefan/7770550/working/building/REAL300000300757 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300757 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300757/0 /scratch/stefan/7770550/working/building/REAL300000300757 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1121) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1121 `/scratch/stefan/7770550/working/3D/1121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(F)(F)F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300757 none COC1=CC(C(F)(F)F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300757 none COC1=CC(C(F)(F)F)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [1, 2, 3, 4, 5, 38, 9, 10, 11, 25, 29, 30] set([0, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 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 /scratch/stefan/7770550/working/building/REAL300000300757 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300757/1 /scratch/stefan/7770550/working/building/REAL300000300757 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1122) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1122 `/scratch/stefan/7770550/working/3D/1122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(F)(F)F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300757.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300757 none COC1=CC(C(F)(F)F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300757 none COC1=CC(C(F)(F)F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [1, 2, 3, 4, 5, 9, 10, 11, 25, 29, 30, 37] set([0, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300757 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300757 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300757/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300757/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300757 Building REAL300000300758 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300758' /scratch/stefan/7770550/working/building/REAL300000300758 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300758 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300758/0 /scratch/stefan/7770550/working/building/REAL300000300758 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1123) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1123 `/scratch/stefan/7770550/working/3D/1123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(OC(C)C)=C1) `REAL300000300758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300758 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(OC(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 9, 12, 19, 19, 19, 19, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 6, 11, 11, 1, 19, 19, 19, 19, 19, 19, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1] 63 rigid atoms, others: [39, 11, 14, 15, 16, 17, 18, 19, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300758 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(OC(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 63, 63, 63, 19, 2, 2, 2, 1, 1, 1, 19, 19, 63, 63, 63, 63, 63, 63, 63, 19] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300758 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300758/1 /scratch/stefan/7770550/working/building/REAL300000300758 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1124) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1124 `/scratch/stefan/7770550/working/3D/1124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(OC(C)C)=C1) `REAL300000300758.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300758 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(OC(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 9, 17, 19, 19, 19, 19, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 6, 13, 13, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1] 71 rigid atoms, others: [32, 40, 11, 14, 15, 16, 17, 18, 19, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 135 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300758 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(OC(C)C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 12, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 71, 71, 71, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 71, 71, 71, 71, 71, 71, 71, 19] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300758 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300758 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300758/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300758/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300758 Building REAL300000300759 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300759' /scratch/stefan/7770550/working/building/REAL300000300759 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300759 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300759/0 /scratch/stefan/7770550/working/building/REAL300000300759 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1125) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1125 `/scratch/stefan/7770550/working/3D/1125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)N=C1) `REAL300000300759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300759 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 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, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 9, 15, 24, 24, 24, 24, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 11, 18, 18, 1, 1, 24, 24, 24, 24, 24, 24, 9, 1, 1, 18, 19, 19, 19, 19, 19, 19, 1] 83 rigid atoms, others: [32, 40, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300759 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(C)C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 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, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 24, 24, 24, 24, 83, 83, 83, 24, 24, 2, 2, 2, 1, 1, 1, 7, 24, 24, 83, 83, 83, 83, 83, 83, 83, 24] 83 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300759 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300759/1 /scratch/stefan/7770550/working/building/REAL300000300759 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1126) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1126 `/scratch/stefan/7770550/working/3D/1126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OC(C)C)N=C1) `REAL300000300759.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300759 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OC(C)C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 9, 17, 28, 28, 28, 28, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 11, 19, 19, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1, 19, 20, 20, 20, 19, 19, 19, 1] 89 rigid atoms, others: [39, 11, 14, 15, 16, 17, 18, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 197 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300759 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(OC(C)C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 28, 28, 28, 28, 89, 89, 89, 28, 28, 2, 2, 2, 1, 1, 1, 28, 28, 89, 89, 89, 89, 89, 89, 89, 28] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300759 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300759 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300759/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300759/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300759 Building REAL300000300760 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300760' /scratch/stefan/7770550/working/building/REAL300000300760 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300760 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300760/0 /scratch/stefan/7770550/working/building/REAL300000300760 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1127) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1127 `/scratch/stefan/7770550/working/3D/1127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1[N+](=O)[O-]) `REAL300000300760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300760 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 5, 5, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 1, 1, 2, 2, 1] 15 rigid atoms, others: [33, 34, 37, 11, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300760 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(CC(=O)[O-])C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 15, 15, 11] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300760 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300760 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300760/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300760 Building REAL300000300761 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300761' /scratch/stefan/7770550/working/building/REAL300000300761 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300761 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300761/0 /scratch/stefan/7770550/working/building/REAL300000300761 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1128) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1128 `/scratch/stefan/7770550/working/3D/1128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)CCC2=C1) `REAL300000300761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300761 none COC1=CC=C2C=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)CCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 79, 79, 79, 18, 8, 18, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 8, 1, 1, 1, 2, 2, 2, 79, 79, 79, 79, 79] 79 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300761 none COC1=CC=C2C=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)CCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 34, 79, 79, 34, 50, 79, 79, 79, 79, 79, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 34, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1] 79 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 39, 43, 40, 22, 23, 24, 25, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300761 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300761 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300761/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300761 Building REAL300000300762 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300762' /scratch/stefan/7770550/working/building/REAL300000300762 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300762 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300762/0 /scratch/stefan/7770550/working/building/REAL300000300762 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1129) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1129 `/scratch/stefan/7770550/working/3D/1129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC2CC2)C=C1) `REAL300000300762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300762 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 5, 9, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 15, 15, 1, 1, 13, 13, 13, 13, 13, 13, 5, 1, 1, 15, 15, 15, 15, 15, 1, 1] 55 rigid atoms, others: [32, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300762 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 39, 55, 55, 13, 13, 2, 2, 2, 1, 1, 1, 7, 13, 13, 55, 55, 55, 55, 55, 13, 13] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 151 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: REAL300000300762 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 31, 55, 55, 55, 55, 55, 31, 15, 14, 15, 15, 13, 15, 15, 6, 1, 1, 1, 1, 15, 15, 55, 55, 55, 55, 55, 55, 31, 15, 15, 1, 1, 1, 1, 1, 15, 15] 55 rigid atoms, others: [33, 34, 35, 36, 37, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 249 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300762 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300762 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300762/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300762 Building REAL300000300763 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300763' /scratch/stefan/7770550/working/building/REAL300000300763 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300763 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300763/0 /scratch/stefan/7770550/working/building/REAL300000300763 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1130) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1130 `/scratch/stefan/7770550/working/3D/1130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC(F)=CC=C2O1) `REAL300000300763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300763 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC(F)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 22, 27, 27, 27, 27, 27, 21, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300763 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC(F)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300763 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300763 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300763/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300763 Building REAL300000300764 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300764' /scratch/stefan/7770550/working/building/REAL300000300764 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300764 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300764/0 /scratch/stefan/7770550/working/building/REAL300000300764 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1131) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1131 `/scratch/stefan/7770550/working/3D/1131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C2=CC=CC=C2S1) `REAL300000300764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300764 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 29, 43, 43, 43, 43, 43, 29, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1] 43 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300764 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 19, 19, 19, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 1, 1, 1, 43, 43, 43, 43] 43 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300764 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300764 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300764/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300764 Building REAL300000300765 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300765' /scratch/stefan/7770550/working/building/REAL300000300765 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300765 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300765/0 /scratch/stefan/7770550/working/building/REAL300000300765 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1132) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1132 `/scratch/stefan/7770550/working/3D/1132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300765 none COC(=O)C1=NC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 29, 45, 29, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 29, 29, 29, 1, 1, 1, 2, 2, 2] 45 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300765 none COC(=O)C1=NC=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 29, 29, 17, 29, 29, 29, 29, 29, 29, 5, 5, 5, 1, 1, 1, 29, 29, 29, 29, 29, 29] 45 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300765 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300765 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300765/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300765 Building REAL300000300766 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300766' /scratch/stefan/7770550/working/building/REAL300000300766 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300766 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300766/0 /scratch/stefan/7770550/working/building/REAL300000300766 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1133) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1133 `/scratch/stefan/7770550/working/3D/1133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300766 none CC1=NSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 26, 27, 28, 29]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300766 none CC1=NSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300766 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300766 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300766/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300766 Building REAL300000300767 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300767' /scratch/stefan/7770550/working/building/REAL300000300767 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300767 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300767/0 /scratch/stefan/7770550/working/building/REAL300000300767 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1134) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1134 `/scratch/stefan/7770550/working/3D/1134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=C(F)C=C1[N+](=O)[O-]) `REAL300000300767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300767 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=C(F)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 15, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 5, 5, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 1, 1] 11 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300767 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=C(F)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 15, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300767 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300767 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300767/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300767 Building REAL300000300768 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300768' /scratch/stefan/7770550/working/building/REAL300000300768 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300768 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300768/0 /scratch/stefan/7770550/working/building/REAL300000300768 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1135) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1135 `/scratch/stefan/7770550/working/3D/1135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC(=O)S1) `REAL300000300768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300768 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC(=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 15, 17, 19, 19, 19, 19, 15, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 15, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300768 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC(=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300768 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300768 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300768/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300768 Building REAL300000300769 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300769' /scratch/stefan/7770550/working/building/REAL300000300769 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300769 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300769/0 /scratch/stefan/7770550/working/building/REAL300000300769 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1136) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1136 `/scratch/stefan/7770550/working/3D/1136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(F)(F)F)=CC=C1[O-]) `REAL300000300769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300769 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(F)(F)F)=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300769 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(F)(F)F)=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300769 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300769/1 /scratch/stefan/7770550/working/building/REAL300000300769 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1137) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1137 `/scratch/stefan/7770550/working/3D/1137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=CC=C1O) `REAL300000300769.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300769 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 21, 21, 35, 35, 35, 35, 21, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 1, 1, 1, 2] 70 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300769 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 1, 35, 35, 35, 70] 70 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300769 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300769 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300769/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300769/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300769 Building REAL300000300770 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300770' /scratch/stefan/7770550/working/building/REAL300000300770 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300770 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300770/0 /scratch/stefan/7770550/working/building/REAL300000300770 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1138) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1138 `/scratch/stefan/7770550/working/3D/1138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSN=C1C1=CC=CC=C1) `REAL300000300770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300770 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSN=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 18, 18, 30, 30, 30, 30, 18, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 30, 30, 30, 30, 30, 30, 1, 4, 4, 4, 4, 4] 30 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300770 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSN=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 1, 1, 1, 30, 30, 30, 30, 30, 30] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300770 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSN=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 20, 21, 30, 30, 30, 30, 20, 9, 4, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 4, 1, 1, 1, 1, 1] 30 rigid atoms, others: [32, 33, 34, 35, 36, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 118 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300770 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300770 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300770/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300770 Building REAL300000300771 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300771' /scratch/stefan/7770550/working/building/REAL300000300771 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300771 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300771/0 /scratch/stefan/7770550/working/building/REAL300000300771 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1139) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1139 `/scratch/stefan/7770550/working/3D/1139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2CC2)C=C1) `REAL300000300771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300771 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 3, 3, 3, 3, 3, 1, 1] 17 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 30 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300771 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 17, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 17, 17, 17, 17, 17, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 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: REAL300000300771 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 17, 17, 17, 17, 9, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 9, 3, 3, 1, 1, 1, 1, 1, 3, 3] 17 rigid atoms, others: [32, 33, 34, 35, 36, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 51 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300771 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300771 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300771/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300771 Building REAL300000300772 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300772' /scratch/stefan/7770550/working/building/REAL300000300772 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300772 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300772/0 /scratch/stefan/7770550/working/building/REAL300000300772 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1140) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1140 `/scratch/stefan/7770550/working/3D/1140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(Cl)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300772 none CCOC(=O)C1=CC(Cl)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 101, 17, 101, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 119, 119, 119, 119, 119, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 119 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300772 none CCOC(=O)C1=CC(Cl)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [25, 18, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 25, 25, 25, 24, 24, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 119 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 40, 25, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300772 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300772/1 /scratch/stefan/7770550/working/building/REAL300000300772 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1141) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1141 `/scratch/stefan/7770550/working/3D/1141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC(Cl)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300772.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300772 none CCOC(=O)C1=CC(Cl)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 91, 17, 91, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 101, 101, 101, 101, 101, 17, 17, 1, 1, 1, 2, 2, 2, 17] 101 rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300772 none CCOC(=O)C1=CC(Cl)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 19, 19, 19, 18, 18, 1, 1, 17, 17, 17, 17, 17, 17, 1] 101 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 25, 39, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300772 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300772 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300772/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300772/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300772 Building REAL300000300773 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300773' /scratch/stefan/7770550/working/building/REAL300000300773 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300773 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300773/0 /scratch/stefan/7770550/working/building/REAL300000300773 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1142) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1142 `/scratch/stefan/7770550/working/3D/1142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CS1) `REAL300000300773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300773 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 33, 45, 45, 45, 45, 45, 33, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 1, 1] 45 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300773 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 45, 45, 45, 45, 45, 2, 2, 2, 1, 1, 1, 45, 45] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300773 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300773 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300773/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300773 Building REAL300000300774 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300774' /scratch/stefan/7770550/working/building/REAL300000300774 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300774 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300774/0 /scratch/stefan/7770550/working/building/REAL300000300774 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1143) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1143 `/scratch/stefan/7770550/working/3D/1143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=CC=C2NC1=O) `REAL300000300774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300774 none CC1=CC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=CC=C2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17] 17 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300774 none CC1=CC2=CC(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=CC=C2NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 20, 21, 22, 23, 24, 25, 38, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300774 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300774 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300774/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300774 Building REAL300000300775 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300775' /scratch/stefan/7770550/working/building/REAL300000300775 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300775 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300775/0 /scratch/stefan/7770550/working/building/REAL300000300775 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1144) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1144 `/scratch/stefan/7770550/working/3D/1144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CN=C1OCC(F)F) `REAL300000300775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300775 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CN=C1OCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 23, 39, 45, 45, 45, 45, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 41, 69, 69, 45, 45, 45, 45, 45, 45, 1, 1, 1, 41, 41, 69] 201 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300775 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CN=C1OCC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 45, 45, 45, 45, 45, 45, 118, 201, 201, 201, 2, 2, 2, 1, 1, 1, 45, 45, 45, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 625 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300775 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300775 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300775/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300775 Building REAL300000300776 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300776' /scratch/stefan/7770550/working/building/REAL300000300776 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300776 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300776/0 /scratch/stefan/7770550/working/building/REAL300000300776 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1145) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1145 `/scratch/stefan/7770550/working/3D/1145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C(F)(F)F) `REAL300000300776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300776 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 9, 13, 13, 13, 13, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300776 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300776 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300776 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300776/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300776 Building REAL300000300777 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300777' /scratch/stefan/7770550/working/building/REAL300000300777 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300777 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300777/0 /scratch/stefan/7770550/working/building/REAL300000300777 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1146) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1146 `/scratch/stefan/7770550/working/3D/1146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=O)CCCC2=C1) `REAL300000300777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300777 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=O)CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 15, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300777 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=O)CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300777 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300777/1 /scratch/stefan/7770550/working/building/REAL300000300777 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1147) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1147 `/scratch/stefan/7770550/working/3D/1147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=O)CCCC2=C1) `REAL300000300777.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300777 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=O)CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300777 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=O)CCCC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300777 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300777 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300777/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300777/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300777 Building REAL300000300778 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300778' /scratch/stefan/7770550/working/building/REAL300000300778 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300778 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300778/0 /scratch/stefan/7770550/working/building/REAL300000300778 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1148) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1148 `/scratch/stefan/7770550/working/3D/1148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C(F)=C1) `REAL300000300778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300778 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300778 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C#N)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300778 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300778/1 /scratch/stefan/7770550/working/building/REAL300000300778 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1149) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1149 `/scratch/stefan/7770550/working/3D/1149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C(F)=C1) `REAL300000300778.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300778 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300778 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C#N)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300778 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300778 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300778/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300778/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300778 Building REAL300000300779 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300779' /scratch/stefan/7770550/working/building/REAL300000300779 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300779 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300779/0 /scratch/stefan/7770550/working/building/REAL300000300779 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1150) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1150 `/scratch/stefan/7770550/working/3D/1150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C)=C([N+](=O)[O-])C=C1F) `REAL300000300779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300779 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C)=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 19, 27, 27, 27, 27, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 1] 27 rigid atoms, others: [35, 11, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300779 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C)=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 19, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300779 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300779 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300779/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300779 Building REAL300000300780 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300780' /scratch/stefan/7770550/working/building/REAL300000300780 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300780 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300780/0 /scratch/stefan/7770550/working/building/REAL300000300780 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1151) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1151 `/scratch/stefan/7770550/working/3D/1151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C) `REAL300000300780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300780 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 9, 15, 19, 19, 19, 19, 9, 5, 1, 5, 5, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300780 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(=O)[O-])=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300780 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300780 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300780/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300780 Building REAL300000300781 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300781' /scratch/stefan/7770550/working/building/REAL300000300781 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300781 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300781/0 /scratch/stefan/7770550/working/building/REAL300000300781 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1152) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1152 `/scratch/stefan/7770550/working/3D/1152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C2=NON=C21) `REAL300000300781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300781 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C2=NON=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 15, 23, 23, 23, 23, 23, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300781 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C2=NON=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300781 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300781 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300781/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300781 Building REAL300000300782 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300782' /scratch/stefan/7770550/working/building/REAL300000300782 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300782 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300782/0 /scratch/stefan/7770550/working/building/REAL300000300782 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1153) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1153 `/scratch/stefan/7770550/working/3D/1153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1[N+](=O)[O-]) `REAL300000300782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300782 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 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, 5, 5, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300782 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300782 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300782 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300782/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300782 Building REAL300000300783 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300783' /scratch/stefan/7770550/working/building/REAL300000300783 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300783 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300783/0 /scratch/stefan/7770550/working/building/REAL300000300783 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1154) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1154 `/scratch/stefan/7770550/working/3D/1154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(OC(F)(F)F)=C1F) `REAL300000300783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300783 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(OC(F)(F)F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 24, 24, 58, 58, 58, 58, 24, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 11, 20, 20, 20, 1, 1, 58, 58, 58, 58, 58, 58, 1, 1, 1] 160 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300783 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(OC(F)(F)F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 58, 58, 58, 58, 58, 160, 160, 160, 160, 58, 58, 2, 2, 2, 1, 1, 1, 58, 58, 58] 160 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300783 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300783 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300783/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300783 Building REAL300000300784 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300784' /scratch/stefan/7770550/working/building/REAL300000300784 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300784 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300784/0 /scratch/stefan/7770550/working/building/REAL300000300784 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1155) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1155 `/scratch/stefan/7770550/working/3D/1155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC(C)=C(Cl)N=C2C=C1) `REAL300000300784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300784 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC(C)=C(Cl)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 16, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 2, 2, 2, 1, 1] 17 rigid atoms, others: [33, 34, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300784 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC(C)=C(Cl)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 16, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300784 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300784 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300784/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300784 Building REAL300000300785 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300785' /scratch/stefan/7770550/working/building/REAL300000300785 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300785 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300785/0 /scratch/stefan/7770550/working/building/REAL300000300785 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1156) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1156 `/scratch/stefan/7770550/working/3D/1156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N=S(C)(C)=O) `REAL300000300785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300785 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N=S(C)(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'C.3', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 14, 5, 5, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 28, 28, 28, 28, 2, 2, 2, 1, 1, 1, 7, 28, 28, 28, 28, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300785 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300785 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300785/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300785 Building REAL300000300786 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300786' /scratch/stefan/7770550/working/building/REAL300000300786 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300786 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300786/0 /scratch/stefan/7770550/working/building/REAL300000300786 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1157) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1157 `/scratch/stefan/7770550/working/3D/1157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C) `REAL300000300786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300786 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 48, 100, 48, 48, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 48, 48, 48, 48, 48, 100, 100, 100, 48, 1, 1, 1, 2, 2, 2, 48, 48, 48, 48] 100 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300786 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 1, 9, 1, 1, 1, 1, 7, 7, 7, 21, 48, 48, 21, 21, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 9, 9, 9, 1, 48, 48, 48, 48, 48, 48, 1, 2, 2, 2] 100 rigid atoms, others: [2, 4, 5, 6, 7, 25, 21, 22, 23, 24, 36, 29] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300786 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300786/1 /scratch/stefan/7770550/working/building/REAL300000300786 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1158) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1158 `/scratch/stefan/7770550/working/3D/1158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C) `REAL300000300786.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300786 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 56, 111, 56, 56, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 111, 111, 111, 56, 7, 1, 1, 1, 2, 2, 2, 56, 56, 56, 56] 111 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300786 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 7, 7, 7, 23, 56, 56, 23, 43, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 9, 9, 9, 1, 23, 56, 56, 56, 56, 56, 56, 1, 2, 2, 2] 111 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 25, 29, 37] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300786 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300786 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300786/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300786/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300786 Building REAL300000300787 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300787' /scratch/stefan/7770550/working/building/REAL300000300787 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300787 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300787/0 /scratch/stefan/7770550/working/building/REAL300000300787 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1159) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1159 `/scratch/stefan/7770550/working/3D/1159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)S1) `REAL300000300787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300787 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 21, 21, 21, 21, 21, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 21, 21, 21, 21, 21, 21, 1, 1] 21 rigid atoms, others: [11, 14, 15, 16, 17, 18, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300787 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300787 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300787 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300787/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300787 Building REAL300000300788 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300788' /scratch/stefan/7770550/working/building/REAL300000300788 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300788 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300788/0 /scratch/stefan/7770550/working/building/REAL300000300788 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1160) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1160 `/scratch/stefan/7770550/working/3D/1160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2OCCCN2N=C1) `REAL300000300788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300788 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2OCCCN2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 5, 5, 5, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 19, 32, 32, 32, 32, 32, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1] 32 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300788 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2OCCCN2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 5, 5, 5, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300788 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300788 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300788/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300788 Building REAL300000300789 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300789' /scratch/stefan/7770550/working/building/REAL300000300789 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300789 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300789/0 /scratch/stefan/7770550/working/building/REAL300000300789 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1161) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1161 `/scratch/stefan/7770550/working/3D/1161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1) `REAL300000300789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300789 none CC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 2, 2, 2] 31 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300789 none CC1=CC(C)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 31, 31, 28, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 1, 2, 2, 2, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300789 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300789 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300789/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300789 Building REAL300000300790 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300790' /scratch/stefan/7770550/working/building/REAL300000300790 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300790 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300790/0 /scratch/stefan/7770550/working/building/REAL300000300790 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1162) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1162 `/scratch/stefan/7770550/working/3D/1162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN=C1C) `REAL300000300790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300790 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 17, 61, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 61, 61, 61, 17, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 61 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300790 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 1, 9, 9, 9, 1, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 61 rigid atoms, others: [2, 35, 4, 5, 6, 7, 21, 22, 23, 24, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300790 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300790/1 /scratch/stefan/7770550/working/building/REAL300000300790 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1163) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1163 `/scratch/stefan/7770550/working/3D/1163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN=C1C) `REAL300000300790.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300790 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 19, 59, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 59, 59, 59, 19, 5, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19] 59 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300790 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 9, 19, 19, 19, 19, 19, 1, 1, 1, 1, 9, 9, 9, 1, 9, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2] 59 rigid atoms, others: [2, 4, 5, 6, 7, 21, 22, 23, 24, 36, 28] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300790 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300790 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300790/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300790/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300790 Building REAL300000300791 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300791' /scratch/stefan/7770550/working/building/REAL300000300791 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300791 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300791/0 /scratch/stefan/7770550/working/building/REAL300000300791 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1164) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1164 `/scratch/stefan/7770550/working/3D/1164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300791 none CCCS(=O)(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 51, 51, 51, 51, 51, 51, 51, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 51 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300791 none CCCS(=O)(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 5, 5, 5, 5, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 51 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 43, 34, 24, 25, 42] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300791 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300791/1 /scratch/stefan/7770550/working/building/REAL300000300791 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1165) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1165 `/scratch/stefan/7770550/working/3D/1165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCS(=O)(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300791.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300791 none CCCS(=O)(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 17, 9, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 51, 51, 51, 51, 51, 51, 51, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17] 51 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300791 none CCCS(=O)(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1] 51 rigid atoms, others: [33, 34, 3, 6, 7, 8, 9, 10, 41, 24, 25, 42] set([0, 1, 2, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300791 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300791 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300791/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300791/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300791 Building REAL300000300792 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300792' /scratch/stefan/7770550/working/building/REAL300000300792 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300792 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300792/0 /scratch/stefan/7770550/working/building/REAL300000300792 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1166) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1166 `/scratch/stefan/7770550/working/3D/1166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)N=C1C) `REAL300000300792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300792 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 11, 17, 17, 17, 17, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 11, 1, 1, 2, 2, 2] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300792 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 8, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300792 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300792/1 /scratch/stefan/7770550/working/building/REAL300000300792 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1167) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1167 `/scratch/stefan/7770550/working/3D/1167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1C) `REAL300000300792.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300792 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 13, 20, 20, 20, 20, 20, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2] 20 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300792 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 20, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300792 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300792 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300792/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300792/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300792 Building REAL300000300793 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300793' /scratch/stefan/7770550/working/building/REAL300000300793 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300793 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300793/0 /scratch/stefan/7770550/working/building/REAL300000300793 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1168) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1168 `/scratch/stefan/7770550/working/3D/1168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(Br)N1C) `REAL300000300793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300793 none CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(Br)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'Br', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 17, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1, 2, 2, 2, 55, 55, 55] 55 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 21, 22, 23, 24, 33, 28, 29, 30, 31]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300793 none CC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(Br)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'Br', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 17, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 12, 12, 12, 32, 55, 55, 34, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 2, 2, 2, 55, 55, 55, 55, 55, 55, 2, 2, 2] 55 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300793 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300793 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300793/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300793 Building REAL300000300794 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300794' /scratch/stefan/7770550/working/building/REAL300000300794 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300794 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300794/0 /scratch/stefan/7770550/working/building/REAL300000300794 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1169) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1169 `/scratch/stefan/7770550/working/3D/1169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C(C)=C1) `REAL300000300794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300794 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 2, 2, 2, 1] 17 rigid atoms, others: [32, 33, 37, 11, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300794 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(F)(F)F)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300794 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300794 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300794/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300794 Building REAL300000300795 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300795' /scratch/stefan/7770550/working/building/REAL300000300795 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300795 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300795/0 /scratch/stefan/7770550/working/building/REAL300000300795 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1170) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1170 `/scratch/stefan/7770550/working/3D/1170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300795 none COC(=O)CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 79, 197, 17, 17, 9, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 197, 197, 197, 79, 79, 9, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 197 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 671 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300795 none COC(=O)CC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 6, 38, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 38, 39, 39, 6, 6, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 197 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 40, 24, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300795 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300795 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300795/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300795 Building REAL300000300796 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300796' /scratch/stefan/7770550/working/building/REAL300000300796 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300796 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300796/0 /scratch/stefan/7770550/working/building/REAL300000300796 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1171) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1171 `/scratch/stefan/7770550/working/3D/1171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2ON=C(Cl)C2=C1) `REAL300000300796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300796 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2ON=C(Cl)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 8, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 11, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300796 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2ON=C(Cl)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 8, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300796 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300796/1 /scratch/stefan/7770550/working/building/REAL300000300796 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1172) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1172 `/scratch/stefan/7770550/working/3D/1172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2ON=C(Cl)C2=C1) `REAL300000300796.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300796 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2ON=C(Cl)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 8, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300796 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2ON=C(Cl)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 8, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300796 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300796 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300796/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300796/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300796 Building REAL300000300797 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300797' /scratch/stefan/7770550/working/building/REAL300000300797 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300797 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300797/0 /scratch/stefan/7770550/working/building/REAL300000300797 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1173) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1173 `/scratch/stefan/7770550/working/3D/1173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC1(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)CC1) `REAL300000300797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300797 none CCOC(=O)CC1(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 187, 69, 187, 30, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 30, 30, 201, 201, 201, 201, 201, 69, 69, 7, 1, 1, 1, 2, 2, 2, 30, 30, 30, 30] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 688 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300797 none CCOC(=O)CC1(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 55, 38, 9, 38, 1, 1, 1, 8, 8, 8, 19, 30, 30, 19, 26, 30, 30, 30, 30, 30, 1, 1, 99, 99, 99, 99, 99, 9, 9, 19, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1] 201 rigid atoms, others: [37, 6, 7, 40, 39, 21, 22, 38, 5] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 479 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300797 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300797 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300797/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300797 Building REAL300000300798 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300798' /scratch/stefan/7770550/working/building/REAL300000300798 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300798 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300798/0 /scratch/stefan/7770550/working/building/REAL300000300798 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1174) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1174 `/scratch/stefan/7770550/working/3D/1174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=NN1C) `REAL300000300798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300798 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21] 21 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300798 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 11, 21, 21, 11, 11, 21, 21, 21, 21, 21, 1, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2] 21 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300798 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300798/1 /scratch/stefan/7770550/working/building/REAL300000300798 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1175) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1175 `/scratch/stefan/7770550/working/3D/1175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=NN1C) `REAL300000300798.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300798 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 8, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21] 21 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 32, 34, 17, 18, 19, 20, 21, 22, 23, 24, 33, 28, 29, 30, 31]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300798 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 21, 21, 9, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2] 21 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300798 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300798 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300798/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300798/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300798 Building REAL300000300799 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300799' /scratch/stefan/7770550/working/building/REAL300000300799 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300799 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300799/0 /scratch/stefan/7770550/working/building/REAL300000300799 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1176) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1176 `/scratch/stefan/7770550/working/3D/1176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300799 none C=CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 7, 1, 1, 1, 2, 2, 2, 15, 15] 15 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300799 none C=CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 15, 9, 15, 15, 15, 15, 15, 15, 1, 1, 3, 3, 3, 1, 1, 9, 15, 15, 15, 15, 15, 15, 1, 1] 15 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 35, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300799 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300799 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300799/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300799 Building REAL300000300800 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300800' /scratch/stefan/7770550/working/building/REAL300000300800 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300800 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300800/0 /scratch/stefan/7770550/working/building/REAL300000300800 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1177) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1177 `/scratch/stefan/7770550/working/3D/1177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300800 none CCN(C)C(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 98, 72, 98, 19, 72, 19, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 162, 162, 162, 162, 162, 98, 98, 98, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2, 19] 162 rigid atoms, others: [38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 687 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300800 none CCN(C)C(=O)C1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [29, 19, 11, 19, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 29, 29, 29, 29, 29, 19, 19, 19, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1] 162 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 44, 25, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300800 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300800/1 /scratch/stefan/7770550/working/building/REAL300000300800 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1178) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1178 `/scratch/stefan/7770550/working/3D/1178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300800.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300800 none CCN(C)C(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 81, 59, 81, 19, 59, 19, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 108, 108, 108, 108, 108, 81, 81, 81, 19, 19, 19, 1, 1, 1, 2, 2, 2, 19] 108 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 412 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300800 none CCN(C)C(=O)C1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 19, 9, 19, 1, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 29, 29, 29, 29, 29, 19, 19, 19, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1] 108 rigid atoms, others: [34, 35, 4, 6, 7, 8, 9, 10, 11, 43, 25, 36] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300800 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300800 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300800/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300800/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300800 Building REAL300000300801 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300801' /scratch/stefan/7770550/working/building/REAL300000300801 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300801 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300801/0 /scratch/stefan/7770550/working/building/REAL300000300801 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1179) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1179 `/scratch/stefan/7770550/working/3D/1179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300801 none CC1=NN(C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2] 21 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300801 none CC1=NN(C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 21, 21, 19, 19, 21, 21, 21, 21, 21, 2, 2, 2, 2, 2, 2, 1, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300801 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300801 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300801/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300801 Building REAL300000300802 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300802' /scratch/stefan/7770550/working/building/REAL300000300802 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300802 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300802/0 /scratch/stefan/7770550/working/building/REAL300000300802 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1180) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1180 `/scratch/stefan/7770550/working/3D/1180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC(Cl)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300802 none COCC1=CC(Cl)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 71, 71, 71, 71, 71, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 71 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300802 none COCC1=CC(Cl)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 22, 22, 22, 7, 7, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 71 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 23, 38, 29, 30] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300802 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300802/1 /scratch/stefan/7770550/working/building/REAL300000300802 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1181) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1181 `/scratch/stefan/7770550/working/3D/1181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC(Cl)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300802.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300802 none COCC1=CC(Cl)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 53, 53, 53, 53, 53, 17, 17, 1, 1, 1, 2, 2, 2, 17] 53 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300802 none COCC1=CC(Cl)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 16, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 13, 17, 17, 17, 17, 17, 1, 12, 12, 12, 7, 7, 1, 1, 17, 17, 17, 17, 17, 17, 1] 53 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 23, 29, 30, 37] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300802 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300802 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300802/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300802/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300802 Building REAL300000300803 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300803' /scratch/stefan/7770550/working/building/REAL300000300803 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300803 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300803/0 /scratch/stefan/7770550/working/building/REAL300000300803 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1182) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1182 `/scratch/stefan/7770550/working/3D/1182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)OC(C)C) `REAL300000300803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300803 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 5, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 120, 120, 152, 153, 153, 27, 27, 27, 27, 27, 7, 1, 1, 1, 2, 2, 2, 27, 153, 153, 153, 153, 153, 153, 153] 153 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300803 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(=O)OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 5, 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 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 27, 27, 9, 17, 27, 27, 27, 27, 27, 1, 1, 1, 13, 13, 29, 41, 41, 2, 2, 2, 1, 1, 9, 27, 27, 27, 27, 27, 27, 1, 41, 41, 41, 41, 41, 41, 41] 153 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 19, 20, 21, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300803 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300803 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300803/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300803 Building REAL300000300804 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300804' /scratch/stefan/7770550/working/building/REAL300000300804 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300804 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300804/0 /scratch/stefan/7770550/working/building/REAL300000300804 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1183) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1183 `/scratch/stefan/7770550/working/3D/1183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNN=C1C(F)(F)F) `REAL300000300804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300804 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNN=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 5, 13, 13, 13, 13, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300804 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNN=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300804 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300804 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300804/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300804 Building REAL300000300805 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300805' /scratch/stefan/7770550/working/building/REAL300000300805 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300805 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300805/0 /scratch/stefan/7770550/working/building/REAL300000300805 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1184) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1184 `/scratch/stefan/7770550/working/3D/1184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=NN1C1=CC=CC=C1) `REAL300000300805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300805 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 23, 45, 59, 59, 59, 59, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 59, 59, 59, 59, 59, 59, 1, 4, 4, 4, 4, 4] 59 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300805 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 21, 21, 21, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 2, 2, 2, 1, 1, 1, 59, 59, 59, 59, 59, 59] 59 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300805 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 35, 59, 59, 59, 59, 59, 35, 17, 4, 17, 17, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 4, 1, 1, 1, 1, 1] 59 rigid atoms, others: [32, 33, 34, 35, 36, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300805 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300805 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300805/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300805 Building REAL300000300806 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300806' /scratch/stefan/7770550/working/building/REAL300000300806 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300806 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300806/0 /scratch/stefan/7770550/working/building/REAL300000300806 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1185) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1185 `/scratch/stefan/7770550/working/3D/1185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC(C(=O)OC)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300806 none COCC1=CC(C(=O)OC)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [113, 79, 17, 17, 17, 17, 17, 65, 65, 65, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 113, 113, 113, 79, 79, 17, 65, 65, 65, 17, 5, 1, 1, 1, 2, 2, 2, 17] 159 rigid atoms, others: [38, 39, 40, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300806 none COCC1=CC(C(=O)OC)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [27, 8, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 27, 27, 27, 8, 8, 1, 12, 12, 12, 1, 9, 17, 17, 17, 17, 17, 17, 1] 159 rigid atoms, others: [32, 2, 3, 4, 5, 6, 44, 10, 11, 12, 36, 26] set([0, 1, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300806 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300806/1 /scratch/stefan/7770550/working/building/REAL300000300806 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1186) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1186 `/scratch/stefan/7770550/working/3D/1186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC(C(=O)OC)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300806.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300806 none COCC1=CC(C(=O)OC)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [72, 64, 17, 17, 17, 17, 17, 50, 50, 50, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 72, 72, 72, 64, 64, 17, 50, 50, 50, 17, 1, 1, 1, 2, 2, 2, 17] 102 rigid atoms, others: [37, 38, 39, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300806 none COCC1=CC(C(=O)OC)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 16, 16, 16, 7, 7, 1, 13, 13, 13, 1, 17, 17, 17, 17, 17, 17, 1] 102 rigid atoms, others: [32, 2, 3, 4, 5, 6, 10, 11, 12, 43, 36, 26] set([0, 1, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300806 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300806 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300806/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300806/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300806 Building REAL300000300807 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300807' /scratch/stefan/7770550/working/building/REAL300000300807 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300807 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300807/0 /scratch/stefan/7770550/working/building/REAL300000300807 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1187) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1187 `/scratch/stefan/7770550/working/3D/1187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C(N(C)C)C=CC=C12) `REAL300000300807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300807 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C(N(C)C)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 11, 15, 15, 15, 15, 15, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1] 15 rigid atoms, others: [34, 35, 36, 11, 44, 45, 14, 15, 16, 17, 18, 19, 20, 43, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300807 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C(N(C)C)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300807 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300807/1 /scratch/stefan/7770550/working/building/REAL300000300807 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1188) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1188 `/scratch/stefan/7770550/working/3D/1188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C(N(C)C)C=CC=C12) `REAL300000300807.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300807 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C(N(C)C)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 7, 13, 13, 13, 13, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1] 13 rigid atoms, others: [33, 34, 35, 42, 11, 44, 14, 15, 16, 17, 18, 19, 20, 43, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300807 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C(N(C)C)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300807 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300807 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300807/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300807/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300807 Building REAL300000300808 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300808' /scratch/stefan/7770550/working/building/REAL300000300808 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300808 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300808/0 /scratch/stefan/7770550/working/building/REAL300000300808 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1189) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1189 `/scratch/stefan/7770550/working/3D/1189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2SC(Cl)=NC2=C1) `REAL300000300808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300808 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2SC(Cl)=NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Cl', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300808 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2SC(Cl)=NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Cl', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300808 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300808/1 /scratch/stefan/7770550/working/building/REAL300000300808 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1190) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1190 `/scratch/stefan/7770550/working/3D/1190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2SC(Cl)=NC2=C1) `REAL300000300808.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300808 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2SC(Cl)=NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Cl', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300808 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2SC(Cl)=NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'Cl', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 16, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300808 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300808 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300808/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300808/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300808 Building REAL300000300809 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300809' /scratch/stefan/7770550/working/building/REAL300000300809 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300809 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300809/0 /scratch/stefan/7770550/working/building/REAL300000300809 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1191) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1191 `/scratch/stefan/7770550/working/3D/1191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300809 none COC1=CC(OC)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 43, 17, 61, 61, 61, 80, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 61, 61, 61, 80, 80, 80, 61, 80, 80, 80, 1, 1, 1, 2, 2, 2, 61] 80 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300809 none COC1=CC(OC)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 1, 1, 7, 7, 7, 25, 61, 61, 25, 32, 61, 61, 61, 61, 61, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 61, 61, 61, 61, 61, 61, 1] 80 rigid atoms, others: [1, 2, 3, 4, 5, 38, 7, 8, 22, 23, 24, 28] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300809 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300809/1 /scratch/stefan/7770550/working/building/REAL300000300809 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1192) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1192 `/scratch/stefan/7770550/working/3D/1192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300809.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300809 none COC1=CC(OC)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 49, 15, 49, 49, 49, 55, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 55, 55, 55, 49, 55, 55, 55, 7, 1, 1, 1, 2, 2, 2, 49] 55 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300809 none COC1=CC(OC)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 4, 1, 1, 7, 7, 7, 25, 49, 49, 25, 41, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 25, 49, 49, 49, 49, 49, 49, 1] 55 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 39, 22, 23, 24, 28] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300809 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300809 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300809/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300809/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300809 Building REAL300000300810 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300810' /scratch/stefan/7770550/working/building/REAL300000300810 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300810 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300810/0 /scratch/stefan/7770550/working/building/REAL300000300810 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1193) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1193 `/scratch/stefan/7770550/working/3D/1193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2ON=C(C3CC3)C2=C1) `REAL300000300810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300810 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2ON=C(C3CC3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 12, 8, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 17, 17, 21, 21, 21, 21, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 21, 21, 21, 21, 21, 21, 1, 6, 7, 7, 7, 7, 1] 37 rigid atoms, others: [32, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300810 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2ON=C(C3CC3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 12, 8, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 37, 37, 21, 21, 2, 2, 2, 1, 1, 1, 21, 37, 37, 37, 37, 37, 21] 37 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300810 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2ON=C(C3CC3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 12, 8, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 21, 9, 7, 9, 9, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 37, 7, 1, 1, 1, 1, 1, 7] 37 rigid atoms, others: [33, 34, 35, 36, 37, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300810 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300810/1 /scratch/stefan/7770550/working/building/REAL300000300810 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1194) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1194 `/scratch/stefan/7770550/working/3D/1194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2ON=C(C3CC3)C2=C1) `REAL300000300810.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300810 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2ON=C(C3CC3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 12, 8, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 9, 17, 18, 18, 18, 18, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 18, 18, 18, 18, 18, 18, 9, 1, 5, 6, 5, 6, 6, 1] 35 rigid atoms, others: [33, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300810 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2ON=C(C3CC3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 12, 8, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 35, 35, 18, 18, 2, 2, 2, 1, 1, 1, 5, 18, 35, 35, 35, 35, 35, 18] 35 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300810 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2ON=C(C3CC3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 12, 8, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 21, 35, 35, 35, 35, 35, 21, 8, 6, 8, 8, 6, 6, 5, 5, 5, 5, 1, 1, 1, 1, 5, 6, 35, 35, 35, 35, 35, 35, 21, 6, 1, 1, 1, 1, 1, 6] 35 rigid atoms, others: [34, 35, 36, 37, 38, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 154 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300810 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300810 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300810/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300810/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300810 Building REAL300000300811 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300811' /scratch/stefan/7770550/working/building/REAL300000300811 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300811 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300811/0 /scratch/stefan/7770550/working/building/REAL300000300811 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1195) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1195 `/scratch/stefan/7770550/working/3D/1195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCC(=O)C2=C1) `REAL300000300811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300811 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300811 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300811 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300811 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300811/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300811 Building REAL300000300812 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300812' /scratch/stefan/7770550/working/building/REAL300000300812 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300812 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300812/0 /scratch/stefan/7770550/working/building/REAL300000300812 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1196) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1196 `/scratch/stefan/7770550/working/3D/1196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1F)NC(=O)O2) `REAL300000300812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300812 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1F)NC(=O)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 13, 27, 27, 27, 27, 27, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1] 27 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300812 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=C(C=C1F)NC(=O)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300812 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300812 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300812/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300812 Building REAL300000300813 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300813' /scratch/stefan/7770550/working/building/REAL300000300813 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300813 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300813/0 /scratch/stefan/7770550/working/building/REAL300000300813 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1197) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1197 `/scratch/stefan/7770550/working/3D/1197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=CC(OC)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300813 none COC(=O)CC1=CC(OC)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 12, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 94, 200, 34, 34, 34, 20, 26, 52, 34, 34, 20, 8, 20, 20, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 200, 200, 200, 94, 94, 34, 52, 52, 52, 34, 34, 8, 1, 1, 1, 2, 2, 2] 200 rigid atoms, others: [39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 818 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300813 none COC(=O)CC1=CC(OC)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 12, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 6, 34, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 5, 5, 5, 13, 34, 34, 14, 23, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6, 1, 3, 3, 3, 1, 1, 13, 34, 34, 34, 34, 34, 34] 200 rigid atoms, others: [32, 4, 5, 6, 7, 8, 10, 11, 12, 13, 36, 37] set([0, 1, 2, 3, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300813 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300813 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300813/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300813 Building REAL300000300814 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300814' /scratch/stefan/7770550/working/building/REAL300000300814 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300814 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300814/0 /scratch/stefan/7770550/working/building/REAL300000300814 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1198) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1198 `/scratch/stefan/7770550/working/3D/1198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl) `REAL300000300814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300814 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 7, 1, 1, 1, 2, 2, 2, 23, 23] 23 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300814 none COC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 9, 17, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 4, 4, 1, 9, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300814 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300814/1 /scratch/stefan/7770550/working/building/REAL300000300814 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1199) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1199 `/scratch/stefan/7770550/working/3D/1199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl) `REAL300000300814.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300814 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2, 23, 23] 23 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300814 none COC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 23, 23, 9, 17, 23, 23, 23, 23, 23, 1, 1, 1, 1, 4, 4, 4, 1, 23, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 19, 20, 21, 22, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300814 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300814 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300814/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300814/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300814 Building REAL300000300815 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300815' /scratch/stefan/7770550/working/building/REAL300000300815 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300815 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300815/0 /scratch/stefan/7770550/working/building/REAL300000300815 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1200) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1200 `/scratch/stefan/7770550/working/3D/1200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F) `REAL300000300815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300815 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 13, 21, 29, 29, 29, 29, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 29, 29, 29, 29, 29, 29, 1, 1, 1] 29 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300815 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300815 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300815/1 /scratch/stefan/7770550/working/building/REAL300000300815 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1201) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1201 `/scratch/stefan/7770550/working/3D/1201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F) `REAL300000300815.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300815 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 13, 27, 31, 31, 31, 31, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 31, 31, 31, 31, 31, 31, 13, 1, 1, 1] 31 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300815 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(C(=O)[O-])=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 7, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300815 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300815 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300815/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300815/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300815 Building REAL300000300816 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300816' /scratch/stefan/7770550/working/building/REAL300000300816 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300816 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300816/0 /scratch/stefan/7770550/working/building/REAL300000300816 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1202) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1202 `/scratch/stefan/7770550/working/3D/1202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)NC=N1) `REAL300000300816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300816 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 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, 34, 46, 55, 55, 55, 55, 34, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 1, 1] 55 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300816 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 55, 55, 55, 55, 55, 2, 2, 2, 1, 1, 1, 55, 55] 55 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300816 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300816 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300816/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300816 Building REAL300000300817 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300817' /scratch/stefan/7770550/working/building/REAL300000300817 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300817 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300817/0 /scratch/stefan/7770550/working/building/REAL300000300817 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1203) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1203 `/scratch/stefan/7770550/working/3D/1203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2N=CSC2=CC=C1) `REAL300000300817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300817 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 19, 27, 31, 31, 31, 31, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1] 31 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300817 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300817 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300817/1 /scratch/stefan/7770550/working/building/REAL300000300817 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1204) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1204 `/scratch/stefan/7770550/working/3D/1204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2N=CSC2=CC=C1) `REAL300000300817.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300817 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', '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, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 15, 27, 27, 27, 27, 27, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 15, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300817 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2N=CSC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', '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, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300817 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300817 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300817/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300817/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300817 Building REAL300000300818 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300818' /scratch/stefan/7770550/working/building/REAL300000300818 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300818 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300818/0 /scratch/stefan/7770550/working/building/REAL300000300818 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1205) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1205 `/scratch/stefan/7770550/working/3D/1205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCOC2=C1) `REAL300000300818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300818 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300818 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300818 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300818/1 /scratch/stefan/7770550/working/building/REAL300000300818 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1206) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1206 `/scratch/stefan/7770550/working/3D/1206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCOC2=C1) `REAL300000300818.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300818 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300818 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCOC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300818 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300818 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300818/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300818/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300818 Building REAL300000300819 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300819' /scratch/stefan/7770550/working/building/REAL300000300819 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300819 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300819/0 /scratch/stefan/7770550/working/building/REAL300000300819 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1207) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1207 `/scratch/stefan/7770550/working/3D/1207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C2=CC=CC=C2C=C1) `REAL300000300819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300819 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 15, 15, 25, 25, 25, 25, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300819 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300819 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300819 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300819/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300819 Building REAL300000300820 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300820' /scratch/stefan/7770550/working/building/REAL300000300820 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300820 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300820/0 /scratch/stefan/7770550/working/building/REAL300000300820 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1208) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1208 `/scratch/stefan/7770550/working/3D/1208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OC(F)(F)O2) `REAL300000300820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300820 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OC(F)(F)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 19, 19, 32, 32, 32, 32, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 1, 1, 1] 32 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300820 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OC(F)(F)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 1, 1, 1, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300820 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300820/1 /scratch/stefan/7770550/working/building/REAL300000300820 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1209) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1209 `/scratch/stefan/7770550/working/3D/1209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OC(F)(F)O2) `REAL300000300820.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300820 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OC(F)(F)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 26, 33, 33, 33, 33, 33, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 21, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300820 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OC(F)(F)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 7, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 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 /scratch/stefan/7770550/working/building/REAL300000300820 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300820 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300820/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300820/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300820 Building REAL300000300821 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300821' /scratch/stefan/7770550/working/building/REAL300000300821 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300821 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300821/0 /scratch/stefan/7770550/working/building/REAL300000300821 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1210) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1210 `/scratch/stefan/7770550/working/3D/1210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(Cl)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300821 none COC(=O)C1=C(Cl)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 30, 47, 30, 30, 30, 30, 30, 30, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 47, 47, 47, 30, 30, 30, 1, 1, 1, 2, 2, 2] 47 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300821 none COC(=O)C1=C(Cl)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 30, 30, 16, 17, 30, 30, 30, 30, 30, 5, 5, 5, 1, 1, 1, 30, 30, 30, 30, 30, 30] 47 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300821 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300821/1 /scratch/stefan/7770550/working/building/REAL300000300821 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1211) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1211 `/scratch/stefan/7770550/working/3D/1211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(Cl)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300821.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300821 none COC(=O)C1=C(Cl)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 35, 19, 19, 19, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 35, 35, 35, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300821 none COC(=O)C1=C(Cl)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 16, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 9, 9, 19, 19, 19, 19, 19, 7, 7, 7, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300821 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300821 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300821/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300821/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300821 Building REAL300000300822 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300822' /scratch/stefan/7770550/working/building/REAL300000300822 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300822 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300822/0 /scratch/stefan/7770550/working/building/REAL300000300822 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1212) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1212 `/scratch/stefan/7770550/working/3D/1212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(CC)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(CC)=C1) `REAL300000300822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300822 none CCC1=CC(CC)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(CC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [53, 16, 16, 26, 26, 26, 32, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 26, 26, 33, 26, 53, 53, 53, 53, 53, 26, 32, 32, 32, 32, 32, 7, 1, 1, 1, 2, 2, 2, 33, 33, 33, 33, 33, 26] 64 rigid atoms, others: [38, 39, 40, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 345 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300822 none CCC1=CC(CC)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(CC)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 6, 1, 1, 7, 7, 7, 14, 26, 26, 14, 22, 26, 26, 26, 26, 26, 1, 1, 6, 1, 5, 5, 5, 5, 5, 1, 6, 6, 6, 6, 6, 14, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6, 1] 64 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 49, 22, 23, 25, 31] set([0, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300822 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300822 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300822/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300822 Building REAL300000300823 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300823' /scratch/stefan/7770550/working/building/REAL300000300823 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300823 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300823/0 /scratch/stefan/7770550/working/building/REAL300000300823 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1213) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1213 `/scratch/stefan/7770550/working/3D/1213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=CC=C1Cl) `REAL300000300823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300823 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 15, 15, 19, 19, 19, 19, 15, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 15, 2, 2, 2, 1, 1, 1] 19 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300823 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300823 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300823/1 /scratch/stefan/7770550/working/building/REAL300000300823 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1214) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1214 `/scratch/stefan/7770550/working/3D/1214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC=C1Cl) `REAL300000300823.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300823 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 15, 15, 23, 23, 23, 23, 15, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1] 23 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 113 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300823 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C)C=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300823 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300823 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300823/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300823/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300823 Building REAL300000300824 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300824' /scratch/stefan/7770550/working/building/REAL300000300824 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300824 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300824/0 /scratch/stefan/7770550/working/building/REAL300000300824 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1215) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1215 `/scratch/stefan/7770550/working/3D/1215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1OC(F)F) `REAL300000300824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300824 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 11, 11, 11, 11, 11, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 11, 11, 11, 11, 1, 1, 1, 9] 11 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300824 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 11, 11, 11, 9, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 9, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300824 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300824/1 /scratch/stefan/7770550/working/building/REAL300000300824 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1216) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1216 `/scratch/stefan/7770550/working/3D/1216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1OC(F)F) `REAL300000300824.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300824 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 17, 17, 17, 17, 17, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 11, 1, 1, 1, 17] 23 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300824 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 7, 7, 7, 17, 17, 17, 7, 17, 17, 17, 18, 23, 23, 2, 2, 2, 1, 1, 1, 5, 17, 7, 17, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300824 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300824 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300824/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300824/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300824 Building REAL300000300825 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300825' /scratch/stefan/7770550/working/building/REAL300000300825 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300825 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300825/0 /scratch/stefan/7770550/working/building/REAL300000300825 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1217) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1217 `/scratch/stefan/7770550/working/3D/1217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCC2) `REAL300000300825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300825 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 21, 24, 29, 29, 29, 29, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300825 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300825 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300825/1 /scratch/stefan/7770550/working/building/REAL300000300825 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1218) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1218 `/scratch/stefan/7770550/working/3D/1218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCC2) `REAL300000300825.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300825 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 27, 31, 31, 31, 31, 31, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 19, 1, 1, 1, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300825 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 7, 31, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300825 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300825 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300825/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300825/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300825 Building REAL300000300826 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300826' /scratch/stefan/7770550/working/building/REAL300000300826 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300826 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300826/0 /scratch/stefan/7770550/working/building/REAL300000300826 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1219) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1219 `/scratch/stefan/7770550/working/3D/1219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300826 none COC(=O)CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 85, 201, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 201, 201, 201, 85, 85, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 201 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 661 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300826 none COC(=O)CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 8, 35, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 35, 35, 35, 8, 8, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 40, 23, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300826 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300826/1 /scratch/stefan/7770550/working/building/REAL300000300826 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1220) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1220 `/scratch/stefan/7770550/working/3D/1220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300826.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300826 none COC(=O)CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 91, 201, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 201, 201, 201, 91, 91, 17, 17, 1, 1, 1, 2, 2, 2, 17] 201 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 664 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300826 none COC(=O)CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 8, 33, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 33, 33, 33, 8, 8, 1, 1, 17, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 39, 23, 24, 25, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300826 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300826 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300826/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300826/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300826 Building REAL300000300827 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300827' /scratch/stefan/7770550/working/building/REAL300000300827 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300827 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300827/0 /scratch/stefan/7770550/working/building/REAL300000300827 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1221) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1221 `/scratch/stefan/7770550/working/3D/1221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC(C)=C2S1) `REAL300000300827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300827 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC(C)=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300827 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC(C)=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 8, 8, 8, 17, 26, 26, 17, 17, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 26, 26, 26, 26, 26, 1, 1, 1, 2, 2, 2] 26 rigid atoms, others: [0, 1, 2, 3, 36, 35, 34, 17, 18, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300827 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300827/1 /scratch/stefan/7770550/working/building/REAL300000300827 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1222) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1222 `/scratch/stefan/7770550/working/3D/1222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC(C)=C2S1) `REAL300000300827.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300827 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC(C)=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 5, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 1, 1, 1, 2, 2, 2, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 82 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300827 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC(C)=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 5, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 16, 25, 25, 16, 16, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 25, 25, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2] 25 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 17, 18, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300827 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300827 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300827/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300827/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300827 Building REAL300000300828 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300828' /scratch/stefan/7770550/working/building/REAL300000300828 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300828 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300828/0 /scratch/stefan/7770550/working/building/REAL300000300828 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1223) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1223 `/scratch/stefan/7770550/working/3D/1223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1OC(F)F) `REAL300000300828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300828 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 11, 11, 11, 11, 11, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 11, 11, 11, 11, 11, 11, 1, 1, 1, 9] 11 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300828 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 11, 11, 11, 9, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 10, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300828 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300828/1 /scratch/stefan/7770550/working/building/REAL300000300828 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1224) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1224 `/scratch/stefan/7770550/working/3D/1224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC=C1OC(F)F) `REAL300000300828.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300828 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 17, 17, 17, 17, 17, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 11, 1, 1, 1, 17] 23 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300828 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=CC=C1OC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 7, 7, 7, 17, 17, 17, 7, 17, 17, 17, 18, 23, 23, 2, 2, 2, 1, 1, 1, 5, 17, 7, 17, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300828 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300828 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300828/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300828/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300828 Building REAL300000300829 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300829' /scratch/stefan/7770550/working/building/REAL300000300829 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300829 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300829/0 /scratch/stefan/7770550/working/building/REAL300000300829 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1225) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1225 `/scratch/stefan/7770550/working/3D/1225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)OC) `REAL300000300829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300829 none CCC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 43, 29, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 43, 44, 48, 48, 48, 48, 48, 43, 29, 29, 7, 1, 1, 1, 2, 2, 2, 44, 44, 44] 48 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 237 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300829 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300829 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300829/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300829 Building REAL300000300830 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300830' /scratch/stefan/7770550/working/building/REAL300000300830 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300830 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300830/0 /scratch/stefan/7770550/working/building/REAL300000300830 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1226) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1226 `/scratch/stefan/7770550/working/3D/1226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CC1=CC=CC=C1)CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300830 none COC(CC1=CC=CC=C1)CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [86, 76, 44, 76, 100, 103, 103, 102, 103, 103, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 86, 86, 86, 76, 100, 100, 103, 103, 103, 103, 103, 44, 44, 7, 1, 1, 1, 2, 2, 2] 103 rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 494 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300830 none COC(CC1=CC=CC=C1)CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 9, 3, 1, 1, 1, 1, 1, 1, 1, 9, 18, 38, 38, 38, 78, 103, 103, 78, 78, 103, 103, 103, 103, 103, 16, 16, 16, 9, 3, 3, 1, 1, 1, 1, 1, 18, 18, 78, 103, 103, 103, 103, 103, 103] 103 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 529 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300830 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300830 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300830/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300830 Building REAL300000300831 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300831' /scratch/stefan/7770550/working/building/REAL300000300831 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300831 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300831/0 /scratch/stefan/7770550/working/building/REAL300000300831 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1227) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1227 `/scratch/stefan/7770550/working/3D/1227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CC(C)C)CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300831 none COC(CC(C)C)CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 54, 36, 54, 55, 55, 55, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 55, 55, 55, 54, 55, 55, 55, 55, 55, 55, 55, 55, 55, 36, 36, 7, 1, 1, 1, 2, 2, 2] 55 rigid atoms, others: [38, 39, 40, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 249 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300831 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300831 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300831/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300831 Building REAL300000300832 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300832' /scratch/stefan/7770550/working/building/REAL300000300832 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300832 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300832/0 /scratch/stefan/7770550/working/building/REAL300000300832 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1228) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1228 `/scratch/stefan/7770550/working/3D/1228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOCC1CC1) `REAL300000300832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300832 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 163, 163, 201, 201, 201, 201, 163, 111, 82, 111, 111, 61, 24, 9, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 163, 82, 82, 61, 61, 9, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 975 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300832 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 32, 40, 78, 128, 201, 201, 2, 2, 2, 1, 1, 1, 5, 32, 32, 40, 40, 128, 128, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300832 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300832 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300832/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300832 Building REAL300000300833 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300833' /scratch/stefan/7770550/working/building/REAL300000300833 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300833 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300833/0 /scratch/stefan/7770550/working/building/REAL300000300833 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1229) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1229 `/scratch/stefan/7770550/working/3D/1229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1) `REAL300000300833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300833 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [17, 17, 21, 21, 21, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 21] 21 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300833 none CC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 21, 21, 14, 14, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2, 1, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 20, 21, 22, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300833 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300833 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300833/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300833 Building REAL300000300834 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300834' /scratch/stefan/7770550/working/building/REAL300000300834 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300834 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300834/0 /scratch/stefan/7770550/working/building/REAL300000300834 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1230) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1230 `/scratch/stefan/7770550/working/3D/1230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C1=CC=CC=C1) `REAL300000300834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300834 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 33, 33, 33, 33, 33] 33 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300834 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 3, 3, 3, 3, 3] 33 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 40, 20, 21, 22, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300834 none COC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 17, 33, 33, 17, 17, 33, 33, 33, 33, 33, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 3, 3, 17, 33, 33, 33, 33, 33, 33, 3, 1, 1, 1, 1, 1] 33 rigid atoms, others: [41, 42, 43, 44, 45, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 196 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300834 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300834 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300834/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300834 Building REAL300000300835 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300835' /scratch/stefan/7770550/working/building/REAL300000300835 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300835 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300835/0 /scratch/stefan/7770550/working/building/REAL300000300835 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1231) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1231 `/scratch/stefan/7770550/working/3D/1231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CN=C1Cl) `REAL300000300835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300835 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 13, 13, 13, 13, 13, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300835 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=CN=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300835 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300835 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300835/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300835 Building REAL300000300836 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300836' /scratch/stefan/7770550/working/building/REAL300000300836 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300836 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300836/0 /scratch/stefan/7770550/working/building/REAL300000300836 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1232) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1232 `/scratch/stefan/7770550/working/3D/1232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)N(C)N=C1) `REAL300000300836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300836 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)N(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 21, 21, 21, 21, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1] 21 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300836 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)N(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300836 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300836 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300836/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300836 Building REAL300000300837 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300837' /scratch/stefan/7770550/working/building/REAL300000300837 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300837 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300837/0 /scratch/stefan/7770550/working/building/REAL300000300837 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1233) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1233 `/scratch/stefan/7770550/working/3D/1233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)N=NN2C) `REAL300000300837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300837 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)N=NN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300837 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2C(=C1)N=NN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300837 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300837/1 /scratch/stefan/7770550/working/building/REAL300000300837 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1234) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1234 `/scratch/stefan/7770550/working/3D/1234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)N=NN2C) `REAL300000300837.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300837 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)N=NN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300837 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2C(=C1)N=NN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300837 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300837 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300837/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300837/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300837 Building REAL300000300838 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300838' /scratch/stefan/7770550/working/building/REAL300000300838 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300838 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300838/0 /scratch/stefan/7770550/working/building/REAL300000300838 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1235) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1235 `/scratch/stefan/7770550/working/3D/1235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N=S(C)(=O)C1=CC=CC=C1) `REAL300000300838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300838 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N=S(C)(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 14, 5, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 47, 47, 65, 65, 65, 65, 47, 27, 7, 27, 27, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 47, 7, 7, 7, 1, 1, 1, 1, 1] 65 rigid atoms, others: [34, 35, 36, 37, 38, 15, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300838 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N=S(C)(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 14, 5, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 51, 51, 51, 51, 65, 65, 65, 65, 65, 2, 2, 2, 1, 1, 1, 8, 51, 51, 51, 65, 65, 65, 65, 65] 65 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300838 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300838 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300838/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300838 Building REAL300000300839 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300839' /scratch/stefan/7770550/working/building/REAL300000300839 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300839 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300839/0 /scratch/stefan/7770550/working/building/REAL300000300839 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1236) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1236 `/scratch/stefan/7770550/working/3D/1236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1) `REAL300000300839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300839 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 5, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 5, 1, 2, 2, 2, 1] 9 rigid atoms, others: [32, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300839 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300839 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300839/1 /scratch/stefan/7770550/working/building/REAL300000300839 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1237) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1237 `/scratch/stefan/7770550/working/3D/1237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1) `REAL300000300839.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300839 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 1] 9 rigid atoms, others: [35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300839 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300839 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300839 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300839/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300839/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300839 Building REAL300000300840 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300840' /scratch/stefan/7770550/working/building/REAL300000300840 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300840 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300840/0 /scratch/stefan/7770550/working/building/REAL300000300840 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1238) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1238 `/scratch/stefan/7770550/working/3D/1238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CC1) `REAL300000300840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300840 none COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 1, 8, 17, 37, 37, 37, 69, 96, 96, 69, 94, 96, 96, 96, 96, 96, 1, 1, 1, 17, 17, 17, 8, 17, 17, 69, 96, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1] 96 rigid atoms, others: [34, 35, 36, 37, 38, 2, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 447 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300840 none COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [74, 63, 43, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 96, 96, 74, 74, 74, 63, 43, 43, 7, 1, 1, 1, 2, 2, 2, 96, 96, 96, 96, 96] 96 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 435 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300840 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300840 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300840/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300840 Building REAL300000300841 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300841' /scratch/stefan/7770550/working/building/REAL300000300841 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300841 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300841/0 /scratch/stefan/7770550/working/building/REAL300000300841 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1239) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1239 `/scratch/stefan/7770550/working/3D/1239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300841 none COC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 43, 43, 43, 35, 43, 43, 43, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 47, 47, 47, 43, 17, 43, 1, 1, 1, 2, 2, 2] 47 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300841 none COC1=CC=C(F)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 43, 43, 25, 25, 43, 43, 43, 43, 43, 4, 4, 4, 1, 1, 1, 43, 43, 43, 43, 43, 43] 47 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300841 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300841/1 /scratch/stefan/7770550/working/building/REAL300000300841 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1240) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1240 `/scratch/stefan/7770550/working/3D/1240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300841.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300841 none COC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 31, 37, 37, 37, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 25, 37, 5, 1, 1, 1, 2, 2, 2] 37 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300841 none COC1=CC=C(F)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 37, 37, 21, 31, 37, 37, 37, 37, 37, 3, 3, 3, 1, 1, 1, 21, 37, 37, 37, 37, 37, 37] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300841 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300841 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300841/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300841/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300841 Building REAL300000300842 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300842' /scratch/stefan/7770550/working/building/REAL300000300842 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300842 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300842/0 /scratch/stefan/7770550/working/building/REAL300000300842 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1241) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1241 `/scratch/stefan/7770550/working/3D/1241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(F)(F)OC2=C1) `REAL300000300842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300842 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(F)(F)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300842 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OC(F)(F)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300842 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300842/1 /scratch/stefan/7770550/working/building/REAL300000300842 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1242) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1242 `/scratch/stefan/7770550/working/3D/1242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2OC(F)(F)OC2=C1) `REAL300000300842.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300842 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2OC(F)(F)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300842 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2OC(F)(F)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300842 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300842 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300842/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300842/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300842 Building REAL300000300843 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300843' /scratch/stefan/7770550/working/building/REAL300000300843 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300843 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300843/0 /scratch/stefan/7770550/working/building/REAL300000300843 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1243) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1243 `/scratch/stefan/7770550/working/3D/1243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-]) `REAL300000300843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300843 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300843 none CCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300843 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300843/1 /scratch/stefan/7770550/working/building/REAL300000300843 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1244) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1244 `/scratch/stefan/7770550/working/3D/1244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-]) `REAL300000300843.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300843 none CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300843 none CCC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1[N+](=O)[O-] 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', '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, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 21, 22, 38, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300843 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300843 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300843/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300843/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300843 Building REAL300000300844 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300844' /scratch/stefan/7770550/working/building/REAL300000300844 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300844 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300844/0 /scratch/stefan/7770550/working/building/REAL300000300844 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1245) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1245 `/scratch/stefan/7770550/working/3D/1245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300844 none COC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 55, 55, 55, 27, 55, 55, 73, 73, 73, 55, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 73, 73, 73, 55, 55, 73, 73, 73, 73, 73, 73, 73, 73, 73, 55, 1, 1, 1, 2, 2, 2] 73 rigid atoms, others: [41, 42, 43, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 370 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300844 none COC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7, 25, 55, 55, 25, 43, 55, 55, 55, 55, 55, 4, 4, 4, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 55, 55, 55, 55, 55, 55] 73 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 10, 11, 12, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300844 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300844/1 /scratch/stefan/7770550/working/building/REAL300000300844 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1246) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1246 `/scratch/stefan/7770550/working/3D/1246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300844.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300844 none COC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 56, 56, 56, 26, 56, 56, 72, 72, 72, 56, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 56, 56, 72, 72, 72, 72, 72, 72, 72, 72, 72, 56, 7, 1, 1, 1, 2, 2, 2] 72 rigid atoms, others: [42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300844 none COC1=CC=C(C(C)(C)C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 7, 7, 25, 56, 56, 36, 45, 56, 56, 56, 56, 56, 4, 4, 4, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 25, 56, 56, 56, 56, 56, 56] 72 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 10, 11, 12, 29, 30] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300844 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300844 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300844/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300844/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300844 Building REAL300000300845 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300845' /scratch/stefan/7770550/working/building/REAL300000300845 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300845 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300845/0 /scratch/stefan/7770550/working/building/REAL300000300845 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1247) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1247 `/scratch/stefan/7770550/working/3D/1247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CCOCC1) `REAL300000300845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300845 none COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 1, 7, 11, 20, 20, 20, 33, 45, 45, 33, 43, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 11, 11, 33, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [2, 37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 212 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300845 none COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 34, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 44, 45, 45, 45, 45, 45, 45, 45, 45, 44, 34, 34, 7, 1, 1, 1, 2, 2, 2, 45, 45, 45, 45, 45, 45, 45, 45, 45] 45 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300845 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300845 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300845/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300845 Building REAL300000300846 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300846' /scratch/stefan/7770550/working/building/REAL300000300846 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300846 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300846/0 /scratch/stefan/7770550/working/building/REAL300000300846 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1248) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1248 `/scratch/stefan/7770550/working/3D/1248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300846 none COC1=NC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300846 none COC1=NC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 20, 21, 22, 23, 24, 25, 26] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300846 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300846/1 /scratch/stefan/7770550/working/building/REAL300000300846 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1249) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1249 `/scratch/stefan/7770550/working/3D/1249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300846.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300846 none COC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300846 none COC1=NC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 20, 21, 22, 23, 24, 25, 26] set([32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300846 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300846 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300846/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300846/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300846 Building REAL300000300847 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300847' /scratch/stefan/7770550/working/building/REAL300000300847 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300847 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300847/0 /scratch/stefan/7770550/working/building/REAL300000300847 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1250) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1250 `/scratch/stefan/7770550/working/3D/1250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(O)=CC(C(F)(F)F)=C1) `REAL300000300847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300847 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(O)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 12, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 2, 1, 1] 34 rigid atoms, others: [32, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 33, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300847 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(O)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 12, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 34, 17, 17] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300847 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300847/1 /scratch/stefan/7770550/working/building/REAL300000300847 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1251) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1251 `/scratch/stefan/7770550/working/3D/1251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(O)=CC(C(F)(F)F)=C1) `REAL300000300847.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300847 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(O)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 12, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 2, 1, 1] 34 rigid atoms, others: [33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300847 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(O)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 12, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 34, 17, 17] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300847 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300847 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300847/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300847/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300847 Building REAL300000300848 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300848' /scratch/stefan/7770550/working/building/REAL300000300848 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300848 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300848/0 /scratch/stefan/7770550/working/building/REAL300000300848 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1252) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1252 `/scratch/stefan/7770550/working/3D/1252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl) `REAL300000300848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300848 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300848 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 33, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300848 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300848 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300848/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300848 Building REAL300000300849 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300849' /scratch/stefan/7770550/working/building/REAL300000300849 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300849 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300849/0 /scratch/stefan/7770550/working/building/REAL300000300849 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1253) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1253 `/scratch/stefan/7770550/working/3D/1253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCC(=O)C2=C1) `REAL300000300849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300849 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300849 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300849 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300849/1 /scratch/stefan/7770550/working/building/REAL300000300849 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1254) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1254 `/scratch/stefan/7770550/working/3D/1254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCC(=O)C2=C1) `REAL300000300849.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300849/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300849 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 16, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300849 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300849 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300849 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300849/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300849/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300849 Building REAL300000300850 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300850' /scratch/stefan/7770550/working/building/REAL300000300850 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300850 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300850/0 /scratch/stefan/7770550/working/building/REAL300000300850 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1255) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1255 `/scratch/stefan/7770550/working/3D/1255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=N1) `REAL300000300850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300850 none CC1=CSC(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 7, 13, 15, 15, 15, 15, 15, 1, 1, 3, 4, 4, 4, 3, 1, 1, 7, 15, 15, 15, 15, 15, 15, 1, 1] 19 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 40, 23, 24, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300850 none CC1=CSC(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 6, 6, 6, 11, 19, 19, 11, 19, 19, 19, 19, 19, 19, 3, 3, 1, 2, 2, 2, 1, 3, 3, 11, 19, 19, 19, 19, 19, 19, 3, 3] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300850 none CC1=CSC(C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 15, 15, 15, 15, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 19, 19, 19, 19, 19, 15, 15, 5, 1, 1, 1, 2, 2, 2, 15, 15] 19 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300850 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300850/1 /scratch/stefan/7770550/working/building/REAL300000300850 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1256) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1256 `/scratch/stefan/7770550/working/3D/1256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2)=N1) `REAL300000300850.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300850 none CC1=CSC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 15, 15, 6, 10, 15, 15, 15, 15, 15, 1, 1, 3, 4, 4, 4, 3, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1] 22 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 23, 24, 38, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300850 none CC1=CSC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 6, 6, 6, 15, 22, 22, 15, 22, 22, 22, 22, 22, 22, 3, 3, 1, 2, 2, 2, 1, 3, 3, 22, 22, 22, 22, 22, 22, 3, 3] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300850 none CC1=CSC(C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 15, 15, 15, 15, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 22, 22, 22, 22, 22, 15, 15, 1, 1, 1, 2, 2, 2, 15, 15] 22 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 62 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300850 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300850 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300850/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300850/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300850 Building REAL300000300851 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300851' /scratch/stefan/7770550/working/building/REAL300000300851 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300851 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300851/0 /scratch/stefan/7770550/working/building/REAL300000300851 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1257) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1257 `/scratch/stefan/7770550/working/3D/1257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C)=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300851 none COC(=O)C1=CC(C)=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 49, 72, 49, 49, 49, 49, 49, 49, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 49, 72, 72, 72, 49, 49, 49, 49, 1, 1, 1, 2, 2, 2, 49] 72 rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300851 none COC(=O)C1=CC(C)=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 5, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 49, 49, 25, 40, 49, 49, 49, 49, 49, 1, 13, 13, 13, 1, 2, 2, 2, 49, 49, 49, 49, 49, 49, 1] 72 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 25, 29, 39] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300851 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300851 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300851/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300851 Building REAL300000300852 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300852' /scratch/stefan/7770550/working/building/REAL300000300852 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300852 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300852/0 /scratch/stefan/7770550/working/building/REAL300000300852 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1258) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1258 `/scratch/stefan/7770550/working/3D/1258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C([N+](=O)[O-])S1) `REAL300000300852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300852 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C([N+](=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 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, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2] 11 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 32, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300852 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C([N+](=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 3, 3, 3, 5, 11, 11, 5, 7, 11, 11, 11, 11, 11, 1, 1, 2, 2, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 22, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300852 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300852 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300852/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300852 Building REAL300000300853 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300853' /scratch/stefan/7770550/working/building/REAL300000300853 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300853 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300853/0 /scratch/stefan/7770550/working/building/REAL300000300853 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1259) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1259 `/scratch/stefan/7770550/working/3D/1259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N=S(C)(=O)N(C)C) `REAL300000300853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300853 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N=S(C)(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'C.3', 'O.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 14, 5, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 56, 56, 56, 56, 75, 75, 2, 2, 2, 1, 1, 1, 8, 56, 56, 56, 75, 75, 75, 75, 75, 75] 75 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300853 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300853 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300853/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300853 Building REAL300000300854 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300854' /scratch/stefan/7770550/working/building/REAL300000300854 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300854 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300854/0 /scratch/stefan/7770550/working/building/REAL300000300854 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1260) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1260 `/scratch/stefan/7770550/working/3D/1260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C=C1C(F)(F)F) `REAL300000300854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300854 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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, 8, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 1, 1] 11 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300854 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(Cl)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 16, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300854 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300854 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300854/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300854 Building REAL300000300855 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300855' /scratch/stefan/7770550/working/building/REAL300000300855 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300855 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300855/0 /scratch/stefan/7770550/working/building/REAL300000300855 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1261) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1261 `/scratch/stefan/7770550/working/3D/1261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)SC2=C1) `REAL300000300855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300855 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300855 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300855 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300855/1 /scratch/stefan/7770550/working/building/REAL300000300855 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1262) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1262 `/scratch/stefan/7770550/working/3D/1262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)SC2=C1) `REAL300000300855.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300855 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300855 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)SC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300855 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300855 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300855/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300855/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300855 Building REAL300000300856 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300856' /scratch/stefan/7770550/working/building/REAL300000300856 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300856 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300856/0 /scratch/stefan/7770550/working/building/REAL300000300856 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1263) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1263 `/scratch/stefan/7770550/working/3D/1263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CN=C1F) `REAL300000300856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300856 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CN=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 14, 18, 18, 18, 18, 18, 9, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 1, 1, 1] 18 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300856 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CN=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1, 1, 1, 18, 18, 18] 18 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300856 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300856 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300856/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300856 Building REAL300000300857 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300857' /scratch/stefan/7770550/working/building/REAL300000300857 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300857 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300857/0 /scratch/stefan/7770550/working/building/REAL300000300857 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1264) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1264 `/scratch/stefan/7770550/working/3D/1264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCC1CCCC1) `REAL300000300857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300857 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 62, 62, 83, 83, 83, 83, 62, 30, 8, 30, 30, 6, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 62, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 83 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 380 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300857 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 46, 54, 83, 83, 83, 83, 2, 2, 2, 1, 1, 1, 7, 46, 46, 54, 54, 83, 83, 83, 83, 83, 83, 83, 83, 83] 83 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 358 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300857 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300857 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300857/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300857 Building REAL300000300858 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300858' /scratch/stefan/7770550/working/building/REAL300000300858 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300858 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300858/0 /scratch/stefan/7770550/working/building/REAL300000300858 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1265) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1265 `/scratch/stefan/7770550/working/3D/1265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)N=C1) `REAL300000300858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300858 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300858 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300858 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300858/1 /scratch/stefan/7770550/working/building/REAL300000300858 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1266) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1266 `/scratch/stefan/7770550/working/3D/1266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)N=C1) `REAL300000300858.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300858 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300858 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(F)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300858 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300858 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300858/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300858/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300858 Building REAL300000300859 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300859' /scratch/stefan/7770550/working/building/REAL300000300859 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300859 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300859/0 /scratch/stefan/7770550/working/building/REAL300000300859 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1267) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1267 `/scratch/stefan/7770550/working/3D/1267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOCC1CCC1) `REAL300000300859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300859 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOCC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 165, 165, 201, 201, 201, 201, 165, 115, 79, 115, 115, 62, 29, 10, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 165, 79, 79, 62, 62, 10, 10, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 954 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300859 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CCOCC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 31, 39, 82, 143, 201, 201, 201, 2, 2, 2, 1, 1, 1, 5, 31, 31, 39, 39, 143, 143, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300859 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300859 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300859/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300859 Building REAL300000300860 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300860' /scratch/stefan/7770550/working/building/REAL300000300860 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300860 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300860/0 /scratch/stefan/7770550/working/building/REAL300000300860 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1268) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1268 `/scratch/stefan/7770550/working/3D/1268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=NC(Cl)=CC=C2S1) `REAL300000300860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300860 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=NC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 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, 13, 18, 21, 21, 21, 21, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1] 21 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300860 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=NC(Cl)=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300860 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300860 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300860/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300860 Building REAL300000300861 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300861' /scratch/stefan/7770550/working/building/REAL300000300861 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300861 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300861/0 /scratch/stefan/7770550/working/building/REAL300000300861 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1269) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1269 `/scratch/stefan/7770550/working/3D/1269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C#N)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300861 none COC(=O)C1=CC(C#N)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 27, 41, 27, 27, 27, 27, 27, 27, 27, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 41, 41, 41, 27, 27, 27, 1, 1, 1, 2, 2, 2] 41 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300861 none COC(=O)C1=CC(C#N)=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 27, 27, 15, 23, 27, 27, 27, 27, 27, 5, 5, 5, 1, 1, 1, 27, 27, 27, 27, 27, 27] 41 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300861 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300861/1 /scratch/stefan/7770550/working/building/REAL300000300861 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1270) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1270 `/scratch/stefan/7770550/working/3D/1270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C#N)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300861.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300861 none COC(=O)C1=CC(C#N)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 19, 35, 19, 19, 15, 19, 19, 19, 19, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 19, 19, 19, 7, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300861 none COC(=O)C1=CC(C#N)=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 19, 19, 11, 19, 19, 19, 19, 19, 19, 7, 7, 7, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300861 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300861 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300861/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300861/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300861 Building REAL300000300862 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300862' /scratch/stefan/7770550/working/building/REAL300000300862 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300862 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300862/0 /scratch/stefan/7770550/working/building/REAL300000300862 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1271) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1271 `/scratch/stefan/7770550/working/3D/1271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C(C)C) `REAL300000300862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300862 none COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 30, 12, 7, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 30, 30, 7, 1, 1, 1, 2, 2, 2, 38, 38, 38, 38, 38, 38, 38] 38 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300862 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300862 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300862/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300862 Building REAL300000300863 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300863' /scratch/stefan/7770550/working/building/REAL300000300863 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300863 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300863/0 /scratch/stefan/7770550/working/building/REAL300000300863 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1272) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1272 `/scratch/stefan/7770550/working/3D/1272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(F)=C1) `REAL300000300863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300863 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300863 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300863 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300863/1 /scratch/stefan/7770550/working/building/REAL300000300863 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1273) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1273 `/scratch/stefan/7770550/working/3D/1273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(F)=C1) `REAL300000300863.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300863 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300863 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300863 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300863 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300863/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300863/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300863 Building REAL300000300864 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300864' /scratch/stefan/7770550/working/building/REAL300000300864 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300864 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300864/0 /scratch/stefan/7770550/working/building/REAL300000300864 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1274) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1274 `/scratch/stefan/7770550/working/3D/1274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCCCO2) `REAL300000300864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300864 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 15, 22, 27, 27, 27, 27, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300864 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300864 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300864/1 /scratch/stefan/7770550/working/building/REAL300000300864 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1275) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1275 `/scratch/stefan/7770550/working/3D/1275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCCCO2) `REAL300000300864.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300864 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 18, 27, 27, 27, 27, 27, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300864 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300864 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300864 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300864/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300864/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300864 Building REAL300000300865 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300865' /scratch/stefan/7770550/working/building/REAL300000300865 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300865 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300865/0 /scratch/stefan/7770550/working/building/REAL300000300865 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1276) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1276 `/scratch/stefan/7770550/working/3D/1276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CS(=O)(=O)CC2=C1) `REAL300000300865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300865 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CS(=O)(=O)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 14, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300865 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CS(=O)(=O)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 14, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300865 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300865/1 /scratch/stefan/7770550/working/building/REAL300000300865 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1277) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1277 `/scratch/stefan/7770550/working/3D/1277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CS(=O)(=O)CC2=C1) `REAL300000300865.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300865 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CS(=O)(=O)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 14, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 11, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300865 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CS(=O)(=O)CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 14, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300865 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300865 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300865/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300865/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300865 Building REAL300000300866 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300866' /scratch/stefan/7770550/working/building/REAL300000300866 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300866 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300866/0 /scratch/stefan/7770550/working/building/REAL300000300866 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1278) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1278 `/scratch/stefan/7770550/working/3D/1278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCCC2) `REAL300000300866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300866 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 25, 31, 31, 31, 31, 31, 18, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300866 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300866 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300866/1 /scratch/stefan/7770550/working/building/REAL300000300866 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1279) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1279 `/scratch/stefan/7770550/working/3D/1279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCCC2) `REAL300000300866.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300866 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 17, 23, 29, 29, 29, 29, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300866 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300866 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300866 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300866/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300866/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300866 Building REAL300000300867 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300867' /scratch/stefan/7770550/working/building/REAL300000300867 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300867 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300867/0 /scratch/stefan/7770550/working/building/REAL300000300867 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1280) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1280 `/scratch/stefan/7770550/working/3D/1280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)C)OC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300867 none CC1=C(C(=O)N(C)C)OC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 12, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [49, 49, 49, 49, 101, 101, 101, 101, 49, 49, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 49, 49, 49, 101, 101, 101, 101, 101, 101, 49, 1, 1, 1, 2, 2, 2] 101 rigid atoms, others: [35, 36, 37, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300867 none CC1=C(C(=O)N(C)C)OC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 12, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 12, 12, 1, 1, 1, 1, 7, 7, 7, 21, 49, 49, 21, 21, 49, 49, 49, 49, 49, 2, 2, 2, 12, 12, 12, 12, 12, 12, 1, 49, 49, 49, 49, 49, 49] 101 rigid atoms, others: [0, 1, 2, 3, 8, 9, 10, 11, 34] set([4, 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, 35, 36, 37, 38, 39, 40]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300867 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300867 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300867/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300867 Building REAL300000300868 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300868' /scratch/stefan/7770550/working/building/REAL300000300868 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300868 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300868/0 /scratch/stefan/7770550/working/building/REAL300000300868 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1281) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1281 `/scratch/stefan/7770550/working/3D/1281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1) `REAL300000300868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300868 none CCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 157, 147, 55, 147, 55, 55, 55, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 55, 55, 55, 162, 162, 162, 162, 162, 55, 55, 1, 1, 1, 2, 2, 2, 55] 162 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 420 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300868 none CCOC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [48, 32, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 7, 23, 55, 55, 23, 24, 55, 55, 55, 55, 55, 1, 1, 1, 48, 48, 48, 48, 48, 1, 1, 55, 55, 55, 55, 55, 55, 1] 162 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 39, 23, 24, 25, 31] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300868 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300868 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300868/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300868 Building REAL300000300869 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300869' /scratch/stefan/7770550/working/building/REAL300000300869 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300869 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300869/0 /scratch/stefan/7770550/working/building/REAL300000300869 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1282) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1282 `/scratch/stefan/7770550/working/3D/1282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCN(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)CC1) `REAL300000300869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300869 none COC1CCN(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 18, 8, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 1, 1, 1, 2, 2, 2, 36, 36, 36, 36] 36 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300869 none COC1CCN(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 36, 36, 19, 28, 36, 36, 36, 36, 36, 1, 1, 6, 6, 6, 1, 1, 1, 1, 1, 18, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1] 36 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 38, 40, 20, 21, 25, 26, 27, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 171 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300869 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300869 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300869/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300869 Building REAL300000300870 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300870' /scratch/stefan/7770550/working/building/REAL300000300870 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300870 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300870/0 /scratch/stefan/7770550/working/building/REAL300000300870 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1283) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1283 `/scratch/stefan/7770550/working/3D/1283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC2=C(C=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)S2)C1) `REAL300000300870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300870 none CC(=O)N1CCC2=C(C=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 30, 35, 30, 30, 30, 30, 30, 30, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 30, 30, 35, 35, 35, 30, 30, 30, 30, 30, 1, 1, 1, 2, 2, 2, 30, 30] 35 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 91 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300870 none CC(=O)N1CCC2=C(C=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 30, 30, 28, 29, 30, 30, 30, 30, 30, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 1, 1] 35 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 40, 41, 24, 25, 33, 29, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300870 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300870 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300870/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300870 Building REAL300000300871 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300871' /scratch/stefan/7770550/working/building/REAL300000300871 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300871 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300871/0 /scratch/stefan/7770550/working/building/REAL300000300871 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1284) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1284 `/scratch/stefan/7770550/working/3D/1284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300871 none COC(=O)C(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 100, 186, 29, 100, 100, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 186, 186, 186, 100, 100, 100, 100, 100, 100, 29, 29, 7, 1, 1, 1, 2, 2, 2, 29, 29] 186 rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300871 none COC(=O)C(C)(C)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 7, 32, 1, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 9, 17, 29, 29, 29, 29, 29, 1, 1, 32, 32, 32, 7, 7, 7, 7, 7, 7, 1, 1, 9, 29, 29, 29, 29, 29, 29, 1, 1] 186 rigid atoms, others: [4, 37, 7, 8, 9, 10, 11, 45, 46, 25, 36, 26] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300871 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300871 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300871/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300871 Building REAL300000300872 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300872' /scratch/stefan/7770550/working/building/REAL300000300872 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300872 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300872/0 /scratch/stefan/7770550/working/building/REAL300000300872 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1285) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1285 `/scratch/stefan/7770550/working/3D/1285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCN(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)CC1) `REAL300000300872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300872 none CCC1CCN(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 47, 47, 47, 47, 20, 8, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 51, 51, 51, 51, 51, 47, 47, 47, 47, 47, 8, 1, 1, 1, 2, 2, 2, 47, 47, 47, 47] 51 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 144 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300872 none CCC1CCN(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 47, 47, 20, 35, 47, 47, 47, 47, 47, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 19, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1] 51 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 41, 42, 20, 21, 27, 28, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 240 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300872 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300872 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300872/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300872 Building REAL300000300873 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300873' /scratch/stefan/7770550/working/building/REAL300000300873 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300873 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300873/0 /scratch/stefan/7770550/working/building/REAL300000300873 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1286) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1286 `/scratch/stefan/7770550/working/3D/1286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(N)=O)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300873 none CC1=CC(C(N)=O)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 29, 29, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 29, 29, 17, 5, 1, 1, 1, 2, 2, 2, 17] 29 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300873 none CC1=CC(C(N)=O)=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 3, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 38, 7, 8, 9, 23, 27, 30] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300873 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300873/1 /scratch/stefan/7770550/working/building/REAL300000300873 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1287) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1287 `/scratch/stefan/7770550/working/3D/1287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(N)=O)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300873.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300873 none CC1=CC(C(N)=O)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 21, 21, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 21, 21, 17, 1, 1, 1, 2, 2, 2, 17] 21 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300873 none CC1=CC(C(N)=O)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 2, 2, 2, 1, 3, 2, 1, 17, 17, 17, 17, 17, 17, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 37, 7, 8, 9, 23, 27, 30] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300873 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300873 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300873/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300873/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300873 Building REAL300000300874 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300874' /scratch/stefan/7770550/working/building/REAL300000300874 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300874 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300874/0 /scratch/stefan/7770550/working/building/REAL300000300874 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1288) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1288 `/scratch/stefan/7770550/working/3D/1288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN(C)C(=O)NC1=O) `REAL300000300874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300874 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN(C)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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, 11, 21, 21, 21, 21, 21, 11, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 11, 1, 2, 2, 2, 1] 21 rigid atoms, others: [34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300874 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN(C)C(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 6, 4, 7, 6, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300874 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300874 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300874/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300874 Building REAL300000300875 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300875' /scratch/stefan/7770550/working/building/REAL300000300875 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300875 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300875/0 /scratch/stefan/7770550/working/building/REAL300000300875 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1289) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1289 `/scratch/stefan/7770550/working/3D/1289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CC1(OC(C)C)CCOC1) `REAL300000300875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300875 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CC1(OC(C)C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 22, 22, 36, 36, 36, 36, 22, 8, 6, 8, 8, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 22, 6, 6, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1] 47 rigid atoms, others: [40, 41, 42, 43, 44, 45, 14, 15, 16, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 194 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300875 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CC1(OC(C)C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 5, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 24, 36, 47, 47, 47, 36, 36, 36, 36, 2, 2, 2, 1, 1, 1, 6, 24, 24, 47, 47, 47, 47, 47, 47, 47, 36, 36, 36, 36, 36, 36] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300875 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300875 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300875/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300875 Building REAL300000300876 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300876' /scratch/stefan/7770550/working/building/REAL300000300876 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300876 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300876/0 /scratch/stefan/7770550/working/building/REAL300000300876 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1290) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1290 `/scratch/stefan/7770550/working/3D/1290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C3C(=C1)CCN3C(=O)CC2) `REAL300000300876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300876 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C3C(=C1)CCN3C(=O)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300876 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=C3C(=C1)CCN3C(=O)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300876 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300876 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300876/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300876 Building REAL300000300877 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300877' /scratch/stefan/7770550/working/building/REAL300000300877 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300877 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300877/0 /scratch/stefan/7770550/working/building/REAL300000300877 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1291) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1291 `/scratch/stefan/7770550/working/3D/1291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C2=CC=C(C)C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=C2)=N1) `REAL300000300877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300877 none CC1=COC(C2=CC=C(C)C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 5, 13, 13, 13, 13, 13, 13, 1, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 5, 13, 13, 13, 13, 13, 13, 1] 23 rigid atoms, others: [32, 43, 4, 5, 6, 7, 8, 9, 10, 11, 25, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 67 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300877 none CC1=COC(C2=CC=C(C)C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 5, 5, 5, 9, 23, 23, 9, 23, 23, 23, 23, 23, 23, 3, 1, 2, 2, 2, 1, 3, 3, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 3] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300877 none CC1=COC(C2=CC=C(C)C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 13, 13, 13, 13, 13, 13, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 23, 23, 23, 23, 23, 13, 13, 13, 13, 13, 8, 1, 1, 1, 2, 2, 2, 13] 23 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 73 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300877 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300877/1 /scratch/stefan/7770550/working/building/REAL300000300877 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1292) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1292 `/scratch/stefan/7770550/working/3D/1292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C2=CC=C(C)C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)=C2)=N1) `REAL300000300877.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300877 none CC1=COC(C2=CC=C(C)C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 13, 13, 7, 9, 13, 13, 13, 13, 13, 1, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 1] 23 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 11, 25, 42, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300877 none CC1=COC(C2=CC=C(C)C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 6, 6, 6, 11, 23, 23, 11, 15, 23, 23, 23, 23, 23, 4, 1, 2, 2, 2, 1, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 4] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300877 none CC1=COC(C2=CC=C(C)C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 13, 13, 13, 13, 13, 13, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 23, 23, 23, 23, 23, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 2, 13] 23 rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 66 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300877 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300877 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300877/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300877/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300877 Building REAL300000300878 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300878' /scratch/stefan/7770550/working/building/REAL300000300878 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300878 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300878/0 /scratch/stefan/7770550/working/building/REAL300000300878 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1293) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1293 `/scratch/stefan/7770550/working/3D/1293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1) `REAL300000300878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300878 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 35, 64, 35, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 64, 64, 64, 1, 1, 1, 2, 2, 2, 35, 35, 35, 35] 64 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300878 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)N(C)N=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 11, 11, 11, 20, 35, 35, 20, 32, 35, 35, 35, 35, 35, 1, 1, 1, 1, 13, 13, 13, 35, 35, 35, 35, 35, 35, 2, 2, 2, 1] 64 rigid atoms, others: [2, 4, 5, 6, 20, 21, 22, 23, 36] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300878 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300878 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300878/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300878 Building REAL300000300879 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300879' /scratch/stefan/7770550/working/building/REAL300000300879 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300879 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300879/0 /scratch/stefan/7770550/working/building/REAL300000300879 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1294) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1294 `/scratch/stefan/7770550/working/3D/1294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300879 none COC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 70, 87, 12, 12, 21, 21, 12, 5, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 87, 87, 87, 70, 21, 21, 5, 1, 1, 1, 2, 2, 2, 21, 21, 21, 21] 89 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300879 none COC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 9, 14, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 12, 17, 21, 21, 21, 21, 21, 1, 1, 1, 14, 14, 14, 9, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2] 89 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 23, 24, 25, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300879 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300879 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300879/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300879 Building REAL300000300880 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300880' /scratch/stefan/7770550/working/building/REAL300000300880 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300880 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300880/0 /scratch/stefan/7770550/working/building/REAL300000300880 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1295) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1295 `/scratch/stefan/7770550/working/3D/1295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C([N+](=O)[O-])C=C1C) `REAL300000300880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300880 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 2, 2, 2] 19 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300880 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(Cl)=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300880 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300880/1 /scratch/stefan/7770550/working/building/REAL300000300880 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1296) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1296 `/scratch/stefan/7770550/working/3D/1296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=C([N+](=O)[O-])C=C1C) `REAL300000300880.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300880 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 17, 22, 28, 28, 28, 28, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1, 2, 2, 2] 28 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300880 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Cl)=C([N+](=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 16, 1, 8, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 1, 1, 1, 28, 28, 28, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300880 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300880 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300880/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300880/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300880 Building REAL300000300881 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300881' /scratch/stefan/7770550/working/building/REAL300000300881 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300881 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300881/0 /scratch/stefan/7770550/working/building/REAL300000300881 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1297) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1297 `/scratch/stefan/7770550/working/3D/1297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300881 none COC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 69, 103, 19, 19, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 103, 103, 103, 69, 19, 19, 5, 1, 1, 1, 2, 2, 2, 19] 103 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300881 none COC(=O)NC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 9, 17, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 1, 1, 17, 17, 17, 9, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1] 103 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 23, 24, 25, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300881 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300881/1 /scratch/stefan/7770550/working/building/REAL300000300881 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1298) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1298 `/scratch/stefan/7770550/working/3D/1298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl) `REAL300000300881.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300881 none COC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 72, 104, 21, 21, 21, 21, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 104, 104, 104, 72, 21, 21, 1, 1, 1, 2, 2, 2, 21] 104 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300881 none COC(=O)NC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [17, 17, 9, 17, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 17, 17, 21, 21, 21, 21, 21, 1, 1, 1, 17, 17, 17, 9, 1, 1, 21, 21, 21, 21, 21, 21, 1] 104 rigid atoms, others: [4, 5, 6, 7, 8, 9, 23, 24, 25, 38, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300881 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300881 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300881/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300881/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300881 Building REAL300000300882 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300882' /scratch/stefan/7770550/working/building/REAL300000300882 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300882 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300882/0 /scratch/stefan/7770550/working/building/REAL300000300882 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1299) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1299 `/scratch/stefan/7770550/working/3D/1299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CC1) `REAL300000300882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300882 none CCOC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 15, 8, 1, 8, 17, 36, 36, 36, 64, 92, 92, 79, 88, 92, 92, 92, 92, 92, 1, 1, 1, 21, 21, 21, 21, 21, 8, 17, 17, 64, 92, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1] 98 rigid atoms, others: [3, 37, 38, 39, 40, 41, 19, 20, 21] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 391 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300882 none CCOC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [94, 91, 79, 49, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 92, 92, 94, 94, 94, 94, 94, 79, 49, 49, 7, 1, 1, 1, 2, 2, 2, 92, 92, 92, 92, 92] 98 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 432 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300882 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300882 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300882/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300882 Building REAL300000300883 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300883' /scratch/stefan/7770550/working/building/REAL300000300883 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300883 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300883/0 /scratch/stefan/7770550/working/building/REAL300000300883 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1300) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1300 `/scratch/stefan/7770550/working/3D/1300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C([N+](=O)[O-])C2=CC=CN=C2C=C1) `REAL300000300883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300883 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C([N+](=O)[O-])C2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 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, 5, 5, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1] 11 rigid atoms, others: [33, 34, 35, 36, 37, 11, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 17, 18, 32, 27, 28, 29, 30, 31]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300883 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C([N+](=O)[O-])C2=CC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300883 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300883 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300883/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300883 Building REAL300000300884 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300884' /scratch/stefan/7770550/working/building/REAL300000300884 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300884 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300884/0 /scratch/stefan/7770550/working/building/REAL300000300884 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1301) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1301 `/scratch/stefan/7770550/working/3D/1301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC2=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=CC=C12) `REAL300000300884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300884 none COC(=O)C1=CC=CC2=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 18, 34, 18, 18, 18, 18, 18, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 34, 34, 34, 18, 18, 18, 7, 1, 1, 1, 2, 2, 2, 18, 18, 18] 34 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300884 none COC(=O)C1=CC=CC2=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 18, 18, 8, 12, 18, 18, 18, 18, 18, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 8, 18, 18, 18, 18, 18, 18, 1, 1, 1] 34 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 43, 41, 24, 25, 26, 27, 42, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300884 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300884/1 /scratch/stefan/7770550/working/building/REAL300000300884 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1302) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1302 `/scratch/stefan/7770550/working/3D/1302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=CC2=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=CC=C12) `REAL300000300884.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300884 none COC(=O)C1=CC=CC2=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 17, 33, 17, 17, 17, 17, 17, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 33, 33, 33, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17, 17] 33 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300884 none COC(=O)C1=CC=CC2=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 17, 17, 7, 9, 17, 17, 17, 17, 17, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 33 rigid atoms, others: [32, 33, 2, 4, 5, 6, 7, 8, 9, 10, 40, 41, 24, 25, 26, 27, 42, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300884 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300884 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300884/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300884/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300884 Building REAL300000300885 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300885' /scratch/stefan/7770550/working/building/REAL300000300885 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300885 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300885/0 /scratch/stefan/7770550/working/building/REAL300000300885 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1303) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1303 `/scratch/stefan/7770550/working/3D/1303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1F) `REAL300000300885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300885 none COC(=O)C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1F 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 54, 86, 54, 54, 54, 54, 54, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 54, 54, 86, 86, 86, 54, 54, 1, 1, 1, 2, 2, 2] 86 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300885 none COC(=O)C1=CC(F)=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1F 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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 54, 54, 25, 25, 54, 54, 54, 54, 54, 1, 1, 10, 10, 10, 1, 1, 54, 54, 54, 54, 54, 54] 86 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 24, 25, 29, 30] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300885 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300885 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300885/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300885 Building REAL300000300886 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300886' /scratch/stefan/7770550/working/building/REAL300000300886 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300886 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300886/0 /scratch/stefan/7770550/working/building/REAL300000300886 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1304) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1304 `/scratch/stefan/7770550/working/3D/1304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300886 none CCC(C)OC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 91, 128, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 128, 128, 128, 128, 128, 128, 128, 128, 128, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 128 rigid atoms, others: [38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 363 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300886 none CCC(C)OC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [30, 25, 13, 25, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 10, 17, 17, 17, 17, 17, 17, 1, 30, 30, 30, 30, 30, 25, 25, 25, 25, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 128 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 44, 24, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300886 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300886/1 /scratch/stefan/7770550/working/building/REAL300000300886 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1305) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1305 `/scratch/stefan/7770550/working/3D/1305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300886.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300886 none CCC(C)OC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 77, 103, 18, 18, 18, 18, 18, 10, 5, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 103, 103, 103, 103, 103, 103, 103, 103, 103, 18, 18, 18, 1, 1, 1, 2, 2, 2, 18] 103 rigid atoms, others: [37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 283 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300886 none CCC(C)OC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 19, 9, 19, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 18, 9, 17, 18, 18, 18, 18, 18, 1, 22, 22, 22, 22, 22, 19, 19, 19, 19, 1, 1, 1, 18, 18, 18, 18, 18, 18, 1] 103 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 43, 24, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300886 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300886 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300886/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300886/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300886 Building REAL300000300887 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300887' /scratch/stefan/7770550/working/building/REAL300000300887 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300887 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300887/0 /scratch/stefan/7770550/working/building/REAL300000300887 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1306) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1306 `/scratch/stefan/7770550/working/3D/1306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CCCC1) `REAL300000300887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300887 none COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 5, 9, 14, 14, 14, 24, 34, 34, 24, 24, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 6, 6, 6, 5, 9, 9, 24, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1] 34 rigid atoms, others: [2, 36, 37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 169 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300887 none COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 28, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 32, 34, 34, 34, 34, 32, 32, 32, 32, 28, 28, 7, 1, 1, 1, 2, 2, 2, 34, 34, 34, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300887 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300887 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300887/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300887 Building REAL300000300888 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300888' /scratch/stefan/7770550/working/building/REAL300000300888 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300888 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300888/0 /scratch/stefan/7770550/working/building/REAL300000300888 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1307) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1307 `/scratch/stefan/7770550/working/3D/1307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CCCCC1) `REAL300000300888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300888 none COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 1, 6, 9, 18, 18, 18, 34, 45, 45, 34, 34, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 9, 9, 34, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [2, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300888 none COC(CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 32, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 44, 45, 45, 45, 45, 45, 45, 45, 45, 44, 32, 32, 6, 1, 1, 1, 2, 2, 2, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45] 45 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300888 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300888 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300888/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300888 Building REAL300000300889 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300889' /scratch/stefan/7770550/working/building/REAL300000300889 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300889 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300889/0 /scratch/stefan/7770550/working/building/REAL300000300889 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1308) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1308 `/scratch/stefan/7770550/working/3D/1308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1CCC1=CC=CC=C1) `REAL300000300889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300889 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [61, 61, 61, 25, 25, 61, 61, 61, 61, 25, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 5, 9, 15, 15, 11, 15, 15, 61, 61, 61, 61, 61, 61, 1, 1, 5, 5, 9, 9, 15, 15, 15, 15, 15] 157 rigid atoms, others: [33, 34, 11, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 355 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300889 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 61, 61, 61, 61, 61, 138, 157, 157, 157, 157, 157, 157, 2, 2, 2, 1, 1, 1, 61, 61, 138, 138, 157, 157, 157, 157, 157, 157, 157] 157 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 32, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 596 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300889 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 101, 101, 157, 157, 157, 157, 101, 46, 15, 46, 46, 15, 15, 15, 15, 5, 3, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 157, 15, 15, 5, 5, 3, 3, 1, 1, 1, 1, 1] 157 rigid atoms, others: [39, 40, 41, 42, 43, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 746 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300889 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300889/1 /scratch/stefan/7770550/working/building/REAL300000300889 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1309) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1309 `/scratch/stefan/7770550/working/3D/1309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=NN1CCC1=CC=CC=C1) `REAL300000300889.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300889 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=NN1CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 57, 57, 24, 44, 57, 57, 57, 57, 24, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 6, 10, 18, 18, 11, 18, 18, 57, 57, 57, 57, 57, 57, 24, 1, 1, 6, 6, 10, 10, 18, 18, 18, 18, 18] 167 rigid atoms, others: [34, 35, 11, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 363 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300889 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=NN1CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 7, 17, 17, 17, 57, 57, 57, 57, 57, 149, 167, 167, 167, 167, 167, 167, 2, 2, 2, 1, 1, 1, 7, 57, 57, 149, 149, 167, 167, 167, 167, 167, 167, 167] 167 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 646 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300889 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=NN1CCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 105, 167, 167, 167, 167, 167, 105, 52, 18, 52, 52, 18, 18, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 105, 18, 18, 6, 6, 4, 4, 1, 1, 1, 1, 1] 167 rigid atoms, others: [40, 41, 42, 43, 44, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 761 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300889 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300889 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300889/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300889/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300889 Building REAL300000300890 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300890' /scratch/stefan/7770550/working/building/REAL300000300890 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300890 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300890/0 /scratch/stefan/7770550/working/building/REAL300000300890 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1310) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1310 `/scratch/stefan/7770550/working/3D/1310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300890 none CC1=CC([N+](=O)[O-])=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 11] 11 rigid atoms, others: [11, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300890 none CC1=CC([N+](=O)[O-])=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 11, 11, 5, 7, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 35, 22, 23, 24, 28] set([5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300890 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300890 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300890/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300890 Building REAL300000300891 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300891' /scratch/stefan/7770550/working/building/REAL300000300891 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300891 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300891/0 /scratch/stefan/7770550/working/building/REAL300000300891 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1311) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1311 `/scratch/stefan/7770550/working/3D/1311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1CC1CC1) `REAL300000300891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300891 none CCC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 121, 192, 192, 133, 133, 133, 133, 133, 1, 1, 1, 2, 2, 2, 43, 121, 121, 192, 192, 192, 192, 192] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 1066 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300891 none CCC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 21, 43, 43, 27, 35, 43, 43, 43, 43, 43, 1, 1, 1, 7, 23, 23, 6, 6, 6, 5, 5, 43, 43, 43, 43, 43, 43, 1, 7, 7, 23, 23, 23, 23, 23] 201 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 21, 36] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) 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: REAL300000300891 none CCC1=NC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN1CC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 23, 23, 23, 23, 23, 75, 75, 75, 138, 192, 192, 155, 182, 192, 192, 192, 192, 192, 23, 9, 1, 1, 1, 1, 44, 44, 44, 44, 44, 192, 192, 192, 192, 192, 192, 23, 9, 9, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 753 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300891 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300891 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300891/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300891 Building REAL300000300892 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300892' /scratch/stefan/7770550/working/building/REAL300000300892 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300892 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300892/0 /scratch/stefan/7770550/working/building/REAL300000300892 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1312) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1312 `/scratch/stefan/7770550/working/3D/1312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(C)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)O1) `REAL300000300892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300892 none COC(=O)C1=C(C)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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, 41, 66, 41, 41, 41, 41, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 66, 66, 66, 41, 41, 41, 41, 1, 1, 1, 2, 2, 2] 66 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300892 none COC(=O)C1=C(C)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 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: [11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 41, 41, 32, 39, 41, 41, 41, 41, 41, 1, 11, 11, 11, 2, 2, 2, 1, 41, 41, 41, 41, 41, 41] 66 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 30] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300892 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300892 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300892/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300892 Building REAL300000300893 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300893' /scratch/stefan/7770550/working/building/REAL300000300893 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300893 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300893/0 /scratch/stefan/7770550/working/building/REAL300000300893 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1313) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1313 `/scratch/stefan/7770550/working/3D/1313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2C1) `REAL300000300893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300893 none CC(=O)N1CC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 33, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 33, 33, 33, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17] 33 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300893 none CC(=O)N1CC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1] 33 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 42, 40, 41, 23, 24, 25, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300893 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300893/1 /scratch/stefan/7770550/working/building/REAL300000300893 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1314) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1314 `/scratch/stefan/7770550/working/3D/1314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2C1) `REAL300000300893.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300893 none CC(=O)N1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 33, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 33, 33, 33, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17, 17] 33 rigid atoms, others: [33, 34, 35, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300893 none CC(=O)N1CC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 33 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 41, 23, 24, 25, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300893 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300893 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300893/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300893/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300893 Building REAL300000300894 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300894' /scratch/stefan/7770550/working/building/REAL300000300894 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300894 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300894/0 /scratch/stefan/7770550/working/building/REAL300000300894 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1315) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1315 `/scratch/stefan/7770550/working/3D/1315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2CC2)S1) `REAL300000300894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300894 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 19, 32, 41, 41, 41, 41, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 13, 12, 1, 41, 41, 41, 41, 41, 41, 1, 12, 13, 13, 13, 13] 82 rigid atoms, others: [11, 14, 15, 16, 17, 18, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 220 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300894 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 7, 17, 17, 17, 41, 41, 41, 41, 82, 82, 41, 2, 2, 2, 1, 1, 1, 41, 82, 82, 82, 82, 82] 82 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300894 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 62, 82, 82, 82, 82, 82, 62, 40, 12, 40, 40, 12, 12, 12, 1, 1, 1, 1, 13, 82, 82, 82, 82, 82, 82, 13, 1, 1, 1, 1, 1] 82 rigid atoms, others: [32, 33, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 314 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300894 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300894 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300894/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300894 Building REAL300000300895 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300895' /scratch/stefan/7770550/working/building/REAL300000300895 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300895 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300895/0 /scratch/stefan/7770550/working/building/REAL300000300895 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1316) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1316 `/scratch/stefan/7770550/working/3D/1316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(C)C) `REAL300000300895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300895 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 144, 70, 13, 13, 21, 21, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 29, 29, 148, 148, 148, 148, 148, 144, 144, 21, 21, 5, 1, 1, 1, 2, 2, 2, 21, 29, 29, 29, 29, 29, 29, 29] 148 rigid atoms, others: [37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 568 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300895 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [29, 27, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 21, 21, 9, 17, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 31, 31, 31, 31, 31, 27, 27, 1, 1, 9, 21, 21, 21, 21, 21, 21, 1, 2, 3, 3, 3, 3, 3, 3] 148 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 43, 35, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 246 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300895 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300895 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300895/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300895 Building REAL300000300896 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300896' /scratch/stefan/7770550/working/building/REAL300000300896 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300896 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300896/0 /scratch/stefan/7770550/working/building/REAL300000300896 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1317) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1317 `/scratch/stefan/7770550/working/3D/1317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C)C([N+](=O)[O-])=C1C) `REAL300000300896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300896 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C)C([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 13, 20, 20, 20, 20, 20, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 20, 20, 20, 20, 20, 20, 13, 1, 1, 2, 2, 2, 2, 2, 2] 20 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300896 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C)C([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 16, 16, 16, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 7, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300896 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300896/1 /scratch/stefan/7770550/working/building/REAL300000300896 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1318) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1318 `/scratch/stefan/7770550/working/3D/1318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C)C([N+](=O)[O-])=C1C) `REAL300000300896.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300896 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C)C([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 17, 27, 27, 27, 27, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 27, 27, 1, 1, 2, 2, 2, 2, 2, 2] 27 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300896 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C)C([N+](=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300896 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300896 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300896/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300896/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300896 Building REAL300000300897 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300897' /scratch/stefan/7770550/working/building/REAL300000300897 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300897 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300897/0 /scratch/stefan/7770550/working/building/REAL300000300897 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1319) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1319 `/scratch/stefan/7770550/working/3D/1319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1) `REAL300000300897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300897 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 9, 11, 11, 11, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [34, 35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300897 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300897 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300897/1 /scratch/stefan/7770550/working/building/REAL300000300897 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1320) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1320 `/scratch/stefan/7770550/working/3D/1320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1) `REAL300000300897.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300897 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 9, 11, 11, 11, 11, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300897 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300897 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300897 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300897/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300897/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300897 Building REAL300000300898 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300898' /scratch/stefan/7770550/working/building/REAL300000300898 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300898 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300898/0 /scratch/stefan/7770550/working/building/REAL300000300898 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1321) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1321 `/scratch/stefan/7770550/working/3D/1321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=NN1C) `REAL300000300898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300898 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 17, 27, 27, 27, 27, 17, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2] 27 rigid atoms, others: [11, 14, 15, 16, 17, 21, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300898 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(F)(F)F)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 15, 15, 15, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300898 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300898 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300898/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300898 Building REAL300000300899 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300899' /scratch/stefan/7770550/working/building/REAL300000300899 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300899 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300899/0 /scratch/stefan/7770550/working/building/REAL300000300899 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1322) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1322 `/scratch/stefan/7770550/working/3D/1322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(SC2=CC=CC=C2)=C1) `REAL300000300899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300899 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(SC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 13, 25, 25, 13, 25, 25, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 25, 25, 13, 25, 25, 1] 179 rigid atoms, others: [34, 35, 36, 42, 11, 14, 15, 16, 17, 18, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300899 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(SC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 157, 179, 179, 157, 179, 179, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 179, 179, 157, 179, 179, 17] 179 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300899 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC(SC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 99, 179, 179, 179, 179, 179, 99, 39, 25, 39, 39, 25, 5, 24, 25, 5, 1, 1, 1, 1, 1, 1, 1, 25, 179, 179, 179, 179, 179, 179, 99, 5, 25, 25, 1, 1, 1, 1, 1, 25] 179 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 877 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300899 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300899/1 /scratch/stefan/7770550/working/building/REAL300000300899 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1323) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1323 `/scratch/stefan/7770550/working/3D/1323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(SC2=CC=CC=C2)=C1) `REAL300000300899.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300899 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(SC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 10, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 13, 29, 29, 15, 29, 29, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 29, 29, 17, 29, 29, 1] 186 rigid atoms, others: [33, 34, 35, 41, 11, 14, 15, 16, 17, 18, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300899 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(SC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 157, 186, 186, 157, 186, 186, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 186, 186, 186, 186, 186, 17] 186 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300899 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(SC2=CC=CC=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 109, 186, 186, 186, 186, 186, 107, 47, 29, 47, 47, 29, 7, 29, 29, 7, 1, 1, 1, 1, 1, 1, 1, 29, 186, 186, 186, 186, 186, 186, 12, 29, 29, 1, 1, 1, 1, 1, 29] 186 rigid atoms, others: [36, 37, 38, 39, 40, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 821 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300899 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300899 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300899/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300899/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300899 Building REAL300000300900 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300900' /scratch/stefan/7770550/working/building/REAL300000300900 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300900 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300900/0 /scratch/stefan/7770550/working/building/REAL300000300900 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1324) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1324 `/scratch/stefan/7770550/working/3D/1324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1F) `REAL300000300900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300900 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 11, 15, 15, 15, 15, 15, 7, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 1, 1] 15 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300900 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Cl)N=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 16, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300900 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300900 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300900/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300900 Building REAL300000300901 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300901' /scratch/stefan/7770550/working/building/REAL300000300901 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300901 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300901/0 /scratch/stefan/7770550/working/building/REAL300000300901 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1325) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1325 `/scratch/stefan/7770550/working/3D/1325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCC3=C2C1=CC=C3) `REAL300000300901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300901 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCC3=C2C1=CC=C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 11, 15, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300901 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2CCC3=C2C1=CC=C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300901 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300901/1 /scratch/stefan/7770550/working/building/REAL300000300901 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1326) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1326 `/scratch/stefan/7770550/working/3D/1326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCC3=C2C1=CC=C3) `REAL300000300901.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300901 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCC3=C2C1=CC=C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 13, 19, 19, 19, 19, 19, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 30, 31]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300901 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2CCC3=C2C1=CC=C3 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300901 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300901 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300901/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300901/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300901 Building REAL300000300902 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300902' /scratch/stefan/7770550/working/building/REAL300000300902 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300902 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300902/0 /scratch/stefan/7770550/working/building/REAL300000300902 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1327) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1327 `/scratch/stefan/7770550/working/3D/1327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1F) `REAL300000300902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300902 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [8, 9, 10, 11, 12, 13, 16, 17, 18, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300902 none CC1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 27, 27, 17, 20, 27, 27, 27, 27, 27, 1, 1, 1, 1, 2, 2, 2, 1, 1, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300902 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300902/1 /scratch/stefan/7770550/working/building/REAL300000300902 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1328) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1328 `/scratch/stefan/7770550/working/3D/1328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1F) `REAL300000300902.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300902 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 1, 1, 1, 2, 2, 2] 27 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300902 none CC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C(F)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 15, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 27, 27, 21, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 2, 2, 2, 1, 1, 15, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300902 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300902 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300902/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300902/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300902 Building REAL300000300903 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300903' /scratch/stefan/7770550/working/building/REAL300000300903 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300903 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300903/0 /scratch/stefan/7770550/working/building/REAL300000300903 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1329) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1329 `/scratch/stefan/7770550/working/3D/1329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)OC=C1) `REAL300000300903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300903 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)OC=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 91, 168, 91, 18, 8, 18, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 91, 91, 91, 168, 168, 168, 1, 1, 1, 2, 2, 2, 91, 91] 168 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300903 none COC(=O)C1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)OC=C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 1, 13, 1, 1, 1, 12, 12, 12, 36, 91, 91, 36, 44, 91, 91, 91, 91, 91, 1, 1, 1, 13, 13, 13, 91, 91, 91, 91, 91, 91, 1, 1] 168 rigid atoms, others: [32, 33, 2, 4, 5, 6, 20, 21, 22] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300903 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300903 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300903/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300903 Building REAL300000300904 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300904' /scratch/stefan/7770550/working/building/REAL300000300904 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300904 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300904/0 /scratch/stefan/7770550/working/building/REAL300000300904 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1330) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1330 `/scratch/stefan/7770550/working/3D/1330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(C)C=C1OC) `REAL300000300904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300904 none CCC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 31, 31, 31, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 23, 17, 47, 59, 59, 59, 59, 59, 31, 7, 1, 1, 1, 2, 2, 2, 31, 31, 31, 31, 47, 47, 47] 59 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 313 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300904 none CCC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(C)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 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 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 5, 5, 5, 13, 31, 31, 13, 23, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 1, 13, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 3, 3, 3] 59 rigid atoms, others: [1, 2, 3, 4, 5, 41, 19, 20, 21, 22, 23, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300904 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300904 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300904/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300904 Building REAL300000300905 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300905' /scratch/stefan/7770550/working/building/REAL300000300905 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300905 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300905/0 /scratch/stefan/7770550/working/building/REAL300000300905 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1331) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1331 `/scratch/stefan/7770550/working/3D/1331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=NN(C)C=C1[N+](=O)[O-]) `REAL300000300905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300905 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=NN(C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 8, 8, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 13, 13, 29, 29, 29, 29, 13, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1] 29 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300905 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=NN(C)C=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 8, 8, 5, 1, 1, 8, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300905 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300905 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300905/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300905 Building REAL300000300906 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300906' /scratch/stefan/7770550/working/building/REAL300000300906 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300906 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300906/0 /scratch/stefan/7770550/working/building/REAL300000300906 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1332) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1332 `/scratch/stefan/7770550/working/3D/1332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(C)=N1) `REAL300000300906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300906 none CCCCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 172, 49, 49, 49, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 49, 49, 49, 201, 201, 201, 201, 201, 201, 201, 172, 172, 49, 1, 1, 1, 2, 2, 2, 49, 49, 49] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 769 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300906 none CCCCN1C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 17, 9, 1, 1, 1, 1, 1, 7, 7, 7, 21, 49, 49, 21, 21, 49, 49, 49, 49, 49, 1, 1, 1, 26, 26, 26, 26, 26, 17, 17, 9, 9, 1, 49, 49, 49, 49, 49, 49, 2, 2, 2] 201 rigid atoms, others: [33, 3, 4, 5, 6, 7, 21, 22, 23] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 364 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300906 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300906 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300906/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300906 Building REAL300000300907 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300907' /scratch/stefan/7770550/working/building/REAL300000300907 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300907 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300907/0 /scratch/stefan/7770550/working/building/REAL300000300907 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1333) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1333 `/scratch/stefan/7770550/working/3D/1333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(OC)C=C1F) `REAL300000300907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300907 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(OC)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 57, 151, 57, 57, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 57, 57, 85, 57, 57, 57, 151, 151, 151, 57, 1, 1, 1, 2, 2, 2, 85, 85, 85, 57] 151 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300907 none COC(=O)C1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C(OC)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 25, 57, 57, 25, 25, 57, 57, 57, 57, 57, 1, 1, 4, 1, 1, 1, 13, 13, 13, 1, 57, 57, 57, 57, 57, 57, 4, 4, 4, 1] 151 rigid atoms, others: [2, 4, 5, 6, 7, 40, 21, 22, 24, 25, 26, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300907 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300907/1 /scratch/stefan/7770550/working/building/REAL300000300907 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1334) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1334 `/scratch/stefan/7770550/working/3D/1334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(OC)C=C1F) `REAL300000300907.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300907 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(OC)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 57, 121, 57, 57, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 69, 57, 57, 57, 121, 121, 121, 57, 7, 1, 1, 1, 2, 2, 2, 69, 69, 69, 57] 121 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300907 none COC(=O)C1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C(OC)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 25, 57, 57, 44, 47, 57, 57, 57, 57, 57, 1, 1, 4, 1, 1, 1, 13, 13, 13, 1, 25, 57, 57, 57, 57, 57, 57, 4, 4, 4, 1] 121 rigid atoms, others: [2, 4, 5, 6, 7, 41, 21, 22, 24, 25, 26, 30] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300907 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300907 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300907/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300907/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300907 Building REAL300000300908 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300908' /scratch/stefan/7770550/working/building/REAL300000300908 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300908 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300908/0 /scratch/stefan/7770550/working/building/REAL300000300908 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1335) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1335 `/scratch/stefan/7770550/working/3D/1335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CC1=CC=C(F)C=C1)CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300908 none COC(CC1=CC=C(F)C=C1)CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [74, 69, 41, 69, 84, 86, 86, 84, 86, 86, 86, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 74, 74, 74, 69, 84, 84, 86, 86, 86, 86, 41, 41, 7, 1, 1, 1, 2, 2, 2] 86 rigid atoms, others: [39, 40, 41, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300908 none COC(CC1=CC=C(F)C=C1)CS(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 35, 35, 35, 66, 86, 86, 66, 66, 86, 86, 86, 86, 86, 12, 12, 12, 8, 3, 3, 1, 1, 1, 1, 18, 18, 66, 86, 86, 86, 86, 86, 86] 86 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300908 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300908 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300908/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300908 Building REAL300000300909 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300909' /scratch/stefan/7770550/working/building/REAL300000300909 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300909 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300909/0 /scratch/stefan/7770550/working/building/REAL300000300909 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1336) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1336 `/scratch/stefan/7770550/working/3D/1336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1) `REAL300000300909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300909 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 15, 20, 30, 30, 30, 30, 15, 7, 1, 7, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 30, 30, 30, 30, 30, 30, 1, 1, 1] 30 rigid atoms, others: [11, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 23, 24, 25, 26, 27, 28]) total number of confs: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300909 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 1, 1, 1, 30, 30, 30] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300909 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300909 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300909/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300909 Building REAL300000300910 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300910' /scratch/stefan/7770550/working/building/REAL300000300910 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300910 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300910/0 /scratch/stefan/7770550/working/building/REAL300000300910 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1337) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1337 `/scratch/stefan/7770550/working/3D/1337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300910 none COC1=C(F)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 39, 39, 39, 39, 39, 39, 1, 1, 1, 2, 2, 2] 39 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300910 none COC1=C(F)C=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 39, 39, 17, 17, 39, 39, 39, 39, 39, 5, 5, 5, 1, 1, 1, 39, 39, 39, 39, 39, 39] 39 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300910 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300910/1 /scratch/stefan/7770550/working/building/REAL300000300910 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1338) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1338 `/scratch/stefan/7770550/working/3D/1338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300910.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300910 none COC1=C(F)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 35, 35, 35, 35, 35, 35, 7, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300910 none COC1=C(F)C=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 35, 35, 19, 29, 35, 35, 35, 35, 35, 3, 3, 3, 1, 1, 1, 17, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300910 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300910 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300910/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300910/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300910 Building REAL300000300911 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300911' /scratch/stefan/7770550/working/building/REAL300000300911 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300911 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300911/0 /scratch/stefan/7770550/working/building/REAL300000300911 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1339) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1339 `/scratch/stefan/7770550/working/3D/1339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(C)C) `REAL300000300911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300911 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 40, 11, 11, 19, 19, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 23, 23, 44, 44, 44, 44, 44, 19, 19, 5, 1, 1, 1, 2, 2, 2, 19, 23, 23, 23, 23, 23, 23, 23] 44 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 172 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300911 none CCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C(C)C 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 1, 1, 2, 2, 9, 9, 9, 9, 9, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1, 2, 3, 3, 3, 2, 2, 2] 44 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 40, 21, 22, 23, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300911 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300911 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300911/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300911 Building REAL300000300912 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300912' /scratch/stefan/7770550/working/building/REAL300000300912 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300912 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300912/0 /scratch/stefan/7770550/working/building/REAL300000300912 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1340) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1340 `/scratch/stefan/7770550/working/3D/1340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(C)(C)C)C(F)=C1) `REAL300000300912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300912 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(C)(C)C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 17 rigid atoms, others: [32, 33, 43, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300912 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C(C)(C)C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300912 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300912/1 /scratch/stefan/7770550/working/building/REAL300000300912 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1341) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1341 `/scratch/stefan/7770550/working/3D/1341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(C)(C)C)C(F)=C1) `REAL300000300912.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300912 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(C)(C)C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1] 17 rigid atoms, others: [32, 36, 37, 38, 42, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 33, 34, 35, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300912 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(C(C)(C)C)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300912 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300912 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300912/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300912/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300912 Building REAL300000300913 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300913' /scratch/stefan/7770550/working/building/REAL300000300913 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300913 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300913/0 /scratch/stefan/7770550/working/building/REAL300000300913 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1342) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1342 `/scratch/stefan/7770550/working/3D/1342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(C#N)=C1) `REAL300000300913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300913 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300913 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300913 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300913/1 /scratch/stefan/7770550/working/building/REAL300000300913 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1343) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1343 `/scratch/stefan/7770550/working/3D/1343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(C#N)=C1) `REAL300000300913.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300913 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300913 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300913 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300913 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300913/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300913/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300913 Building REAL300000300914 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300914' /scratch/stefan/7770550/working/building/REAL300000300914 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300914 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300914/0 /scratch/stefan/7770550/working/building/REAL300000300914 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1344) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1344 `/scratch/stefan/7770550/working/3D/1344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C(F)(F)F)N(C)N=C1) `REAL300000300914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300914 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C(F)(F)F)N(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 15, 15, 15, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 5, 13, 13, 13, 13, 5, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1] 13 rigid atoms, others: [33, 11, 14, 15, 16, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300914 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(C(F)(F)F)N(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 15, 15, 15, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 13, 13, 13, 13] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300914 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300914 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300914/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300914 Building REAL300000300915 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300915' /scratch/stefan/7770550/working/building/REAL300000300915 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300000300915 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300915/0 /scratch/stefan/7770550/working/building/REAL300000300915 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1345) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1345 `/scratch/stefan/7770550/working/3D/1345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2NC=NC=C12) `REAL300000300915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300915 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2NC=NC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 27, 32, 32, 32, 32, 32, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1] 32 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300915 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2NC=NC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 14, 14, 14, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 1, 1, 1, 32, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300915 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300915/1 /scratch/stefan/7770550/working/building/REAL300000300915 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1346) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1346 `/scratch/stefan/7770550/working/3D/1346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC2=NC=NC=C12) `REAL300000300915.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300915 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC2=NC=NC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 17, 23, 23, 23, 23, 23, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 23 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300915 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC2=NC=NC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300915 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `2' /scratch/stefan/7770550/working/building/REAL300000300915/2 /scratch/stefan/7770550/working/building/REAL300000300915 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 2 (index: 1347) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1347 `/scratch/stefan/7770550/working/3D/1347' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC2=NC=NC=C12) `REAL300000300915.mol2' -> `2.mol2' `temp.mol2' -> `REAL300000300915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300915/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300915 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC2=NC=NC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 21, 25, 25, 25, 25, 25, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 21, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300915 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC2=NC=NC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 7, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300915 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300915 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 2: /scratch/stefan/7770550/working/building/REAL300000300915/2.* 1: /scratch/stefan/7770550/working/building/REAL300000300915/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300915/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300915 Building REAL300000300916 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300916' /scratch/stefan/7770550/working/building/REAL300000300916 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300916 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300916/0 /scratch/stefan/7770550/working/building/REAL300000300916 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1348) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1348 `/scratch/stefan/7770550/working/3D/1348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC2=CC=CC=C12) `REAL300000300916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300916 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 21, 21, 28, 28, 28, 28, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300916 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 1, 1, 1, 28, 28, 28, 28, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300916 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300916/1 /scratch/stefan/7770550/working/building/REAL300000300916 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1349) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1349 `/scratch/stefan/7770550/working/3D/1349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC2=CC=CC=C12) `REAL300000300916.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300916 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 21, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300916 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CNC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300916 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300916 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300916/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300916/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300916 Building REAL300000300917 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300917' /scratch/stefan/7770550/working/building/REAL300000300917 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300917 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300917/0 /scratch/stefan/7770550/working/building/REAL300000300917 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1350) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1350 `/scratch/stefan/7770550/working/3D/1350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2CCCCC2=NN1C) `REAL300000300917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300917 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2CCCCC2=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 23, 39, 39, 39, 39, 39, 23, 10, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 39 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300917 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2CCCCC2=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300917 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300917/1 /scratch/stefan/7770550/working/building/REAL300000300917 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1351) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1351 `/scratch/stefan/7770550/working/3D/1351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2CCCCC2=NN1C) `REAL300000300917.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300917 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2CCCCC2=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 22, 40, 40, 40, 40, 40, 22, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 22, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 40 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300917 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2CCCCC2=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 16, 16, 16, 40, 40, 40, 40, 40, 40, 40, 40, 40, 2, 2, 2, 1, 1, 1, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 40 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300917 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300917 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300917/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300917/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300917 Building REAL300000300918 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300918' /scratch/stefan/7770550/working/building/REAL300000300918 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300918 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300918/0 /scratch/stefan/7770550/working/building/REAL300000300918 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1352) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1352 `/scratch/stefan/7770550/working/3D/1352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C(C)(C)C) `REAL300000300918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300918 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 9, 14, 14, 14, 14, 14, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 14 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300918 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300918 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300918 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300918/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300918 Building REAL300000300919 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300919' /scratch/stefan/7770550/working/building/REAL300000300919 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300919 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300919/0 /scratch/stefan/7770550/working/building/REAL300000300919 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1353) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1353 `/scratch/stefan/7770550/working/3D/1353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCCC2)N=C1) `REAL300000300919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300919 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 17, 17, 17, 17, 17, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 72 rigid atoms, others: [40, 11, 14, 15, 16, 17, 22, 23, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 48 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300919 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 72, 72, 72, 72, 17, 17, 2, 2, 2, 1, 1, 1, 17, 72, 72, 72, 72, 72, 72, 72, 72, 72, 17] 72 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300919 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 72, 72, 38, 12, 7, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 72, 72, 72, 72, 72, 72, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7] 72 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40]) total number of confs: 142 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300919 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300919 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300919/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300919 Building REAL300000300920 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300920' /scratch/stefan/7770550/working/building/REAL300000300920 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300920 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300920/0 /scratch/stefan/7770550/working/building/REAL300000300920 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1354) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1354 `/scratch/stefan/7770550/working/3D/1354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1Br) `REAL300000300920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300920 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 17, 17, 27, 27, 27, 27, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2] 27 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300920 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300920 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300920 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300920/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300920 Building REAL300000300921 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300921' /scratch/stefan/7770550/working/building/REAL300000300921 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300921 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300921/0 /scratch/stefan/7770550/working/building/REAL300000300921 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1355) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1355 `/scratch/stefan/7770550/working/3D/1355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1(COCC2=CC=CC=C2)CC1) `REAL300000300921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300921 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1(COCC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 15, 15, 21, 21, 21, 21, 15, 7, 1, 7, 7, 1, 1, 8, 18, 62, 100, 100, 74, 100, 100, 1, 1, 21, 21, 21, 21, 21, 21, 15, 8, 8, 62, 62, 100, 100, 100, 100, 100, 1, 1, 1, 1] 201 rigid atoms, others: [43, 42, 11, 44, 45, 14, 15, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 491 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300921 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1(COCC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 21, 58, 113, 201, 201, 201, 201, 201, 201, 21, 21, 2, 2, 2, 1, 1, 1, 6, 58, 58, 201, 201, 201, 201, 201, 201, 201, 21, 21, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300921 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1(COCC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 190, 190, 201, 201, 201, 201, 190, 154, 100, 154, 154, 42, 18, 4, 1, 1, 1, 1, 1, 1, 1, 100, 100, 201, 201, 201, 201, 201, 201, 190, 42, 42, 4, 4, 1, 1, 1, 1, 1, 100, 100, 100, 100] 201 rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45]) total number of confs: 823 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300921 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300921 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300921/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300921 Building REAL300000300922 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300922' /scratch/stefan/7770550/working/building/REAL300000300922 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300922 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300922/0 /scratch/stefan/7770550/working/building/REAL300000300922 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1356) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1356 `/scratch/stefan/7770550/working/3D/1356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1[O-]) `REAL300000300922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300922 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1] 11 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300922 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300922 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300922/1 /scratch/stefan/7770550/working/building/REAL300000300922 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1357) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1357 `/scratch/stefan/7770550/working/3D/1357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1O) `REAL300000300922.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300922 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 17, 27, 29, 29, 29, 29, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 1, 1, 1, 2] 58 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300922 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 19, 29, 58] 58 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300922 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300922 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300922/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300922/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300922 Building REAL300000300923 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300923' /scratch/stefan/7770550/working/building/REAL300000300923 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300923 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300923/0 /scratch/stefan/7770550/working/building/REAL300000300923 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1358) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1358 `/scratch/stefan/7770550/working/3D/1358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1) `REAL300000300923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300923 none C=CCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 45, 29, 29, 29, 29, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 77, 77, 77, 77, 77, 45, 45, 29, 29, 7, 1, 1, 1, 2, 2, 2, 29, 29] 77 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300923 none C=CCCC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 29, 29, 9, 17, 29, 29, 29, 29, 29, 1, 1, 9, 9, 9, 6, 6, 4, 4, 1, 1, 9, 29, 29, 29, 29, 29, 29, 1, 1] 77 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 41, 40, 22, 23, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300923 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300923 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300923/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300923 Building REAL300000300924 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300924' /scratch/stefan/7770550/working/building/REAL300000300924 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300924 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300924/0 /scratch/stefan/7770550/working/building/REAL300000300924 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1359) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1359 `/scratch/stefan/7770550/working/3D/1359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300924 none COC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 96, 173, 96, 96, 96, 96, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 173, 173, 173, 96, 96, 1, 1, 1, 2, 2, 2] 173 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 21, 22, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 444 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300924 none COC(=O)C1=CNN=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 8, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 37, 96, 96, 37, 39, 96, 96, 96, 96, 96, 13, 13, 13, 1, 1, 96, 96, 96, 96, 96, 96] 173 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300924 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300924 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300924/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300924 Building REAL300000300925 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300925' /scratch/stefan/7770550/working/building/REAL300000300925 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300925 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300925/0 /scratch/stefan/7770550/working/building/REAL300000300925 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1360) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1360 `/scratch/stefan/7770550/working/3D/1360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300925 none CCC1=NN(C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 43, 43, 43, 43, 43, 43, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 55, 55, 55, 55, 55, 43, 43, 43, 43, 1, 1, 1, 2, 2, 2] 55 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300925 none CCC1=NN(C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 43, 43, 21, 29, 43, 43, 43, 43, 43, 6, 6, 6, 5, 5, 2, 2, 2, 1, 43, 43, 43, 43, 43, 43] 55 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300925 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300925 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300925/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300925 Building REAL300000300926 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300926' /scratch/stefan/7770550/working/building/REAL300000300926 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300926 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300926/0 /scratch/stefan/7770550/working/building/REAL300000300926 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1361) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1361 `/scratch/stefan/7770550/working/3D/1361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300926 none CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 19, 39, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 39, 39, 39, 19, 19, 7, 1, 1, 1, 2, 2, 2, 19] 39 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) total number of confs: 133 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300926 none CC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 17, 17, 19, 19, 19, 19, 19, 1, 1, 1, 6, 6, 6, 1, 1, 9, 19, 19, 19, 19, 19, 19, 1] 39 rigid atoms, others: [1, 3, 4, 5, 6, 7, 21, 22, 23, 36, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300926 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300926/1 /scratch/stefan/7770550/working/building/REAL300000300926 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1362) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1362 `/scratch/stefan/7770550/working/3D/1362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300926.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300926 none CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 19, 39, 19, 19, 19, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 39, 39, 39, 19, 19, 1, 1, 1, 2, 2, 2, 19] 39 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 126 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300926 none CC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 17, 19, 19, 19, 19, 19, 1, 1, 1, 5, 5, 5, 1, 1, 19, 19, 19, 19, 19, 19, 1] 39 rigid atoms, others: [1, 3, 4, 5, 6, 7, 35, 21, 22, 23, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 94 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300926 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300926 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300926/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300926/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300926 Building REAL300000300927 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300927' /scratch/stefan/7770550/working/building/REAL300000300927 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300927 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300927/0 /scratch/stefan/7770550/working/building/REAL300000300927 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1363) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1363 `/scratch/stefan/7770550/working/3D/1363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(N)N=C1) `REAL300000300927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300927 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(N)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 9 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300927 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(N)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300927 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300927/1 /scratch/stefan/7770550/working/building/REAL300000300927 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1364) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1364 `/scratch/stefan/7770550/working/3D/1364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C(N)N=C1) `REAL300000300927.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300927 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C(N)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 2, 2, 1] 9 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300927 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C(N)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 24, 25, 26] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300927 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300927 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300927/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300927/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300927 Building REAL300000300928 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300928' /scratch/stefan/7770550/working/building/REAL300000300928 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300928 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300928/0 /scratch/stefan/7770550/working/building/REAL300000300928 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1365) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1365 `/scratch/stefan/7770550/working/3D/1365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(C(F)F)=C1) `REAL300000300928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300928 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 9, 1] 33 rigid atoms, others: [32, 34, 11, 14, 15, 16, 17, 18, 19, 20, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300928 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(F)C(C(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 9, 17, 17, 17, 33, 33, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 33, 17] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300928 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300928 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300928/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300928 Building REAL300000300929 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300929' /scratch/stefan/7770550/working/building/REAL300000300929 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300929 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300929/0 /scratch/stefan/7770550/working/building/REAL300000300929 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1366) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1366 `/scratch/stefan/7770550/working/3D/1366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N=S(=O)(C1=CC=CC=C1)N(C)C) `REAL300000300929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300929 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N=S(=O)(C1=CC=CC=C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 14, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 57, 36, 36, 57, 57, 57, 57, 36, 21, 6, 21, 21, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 9, 9, 57, 57, 57, 57, 57, 57, 36, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9] 57 rigid atoms, others: [33, 34, 35, 36, 37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300929 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N=S(=O)(C1=CC=CC=C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.2', 'S.o', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 14, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 19, 54, 54, 54, 57, 57, 54, 57, 57, 54, 54, 54, 2, 2, 2, 1, 1, 1, 8, 57, 57, 54, 57, 57, 54, 54, 54, 54, 54, 54] 57 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300929 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300929 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300929/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300929 Building REAL300000300930 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300930' /scratch/stefan/7770550/working/building/REAL300000300930 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300930 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300930/0 /scratch/stefan/7770550/working/building/REAL300000300930 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1367) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1367 `/scratch/stefan/7770550/working/3D/1367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C=CC1=CC=CC(Cl)=C1) `REAL300000300930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300930 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C=CC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 159, 194, 194, 194, 194, 194, 148, 78, 11, 78, 78, 11, 1, 1, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 194, 148, 11, 11, 1, 1, 1, 1] 194 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 719 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300930 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C=CC1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 19, 19, 19, 94, 94, 194, 194, 194, 194, 194, 194, 2, 2, 2, 1, 1, 1, 8, 94, 94, 194, 194, 194, 194] 194 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 426 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300930 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300930 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300930/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300930 Building REAL300000300931 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300931' /scratch/stefan/7770550/working/building/REAL300000300931 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300931 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300931/0 /scratch/stefan/7770550/working/building/REAL300000300931 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1368) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1368 `/scratch/stefan/7770550/working/3D/1368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1CC) `REAL300000300931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300931 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1CC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 130, 50, 9, 9, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 137, 137, 137, 137, 137, 130, 130, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 50, 50, 50, 50, 50] 201 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 667 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300931 none CCCOC1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1CC 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 26, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1, 6, 30, 30, 30, 30, 30, 26, 26, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 8, 42, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300931 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300931 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300931/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300931 Building REAL300000300932 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300932' /scratch/stefan/7770550/working/building/REAL300000300932 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300932 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300932/0 /scratch/stefan/7770550/working/building/REAL300000300932 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1369) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1369 `/scratch/stefan/7770550/working/3D/1369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCC#N)C=C1) `REAL300000300932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300932 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 9, 9, 9, 9, 9, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 3, 3, 7, 7, 1, 1] 43 rigid atoms, others: [32, 37, 38, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300932 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(CCC#N)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.1', 'N.1', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 17, 43, 43, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 17, 17, 43, 43, 9, 9] 43 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300932 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300932 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300932/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300932 Building REAL300000300933 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300933' /scratch/stefan/7770550/working/building/REAL300000300933 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300933 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300933/0 /scratch/stefan/7770550/working/building/REAL300000300933 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1370) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1370 `/scratch/stefan/7770550/working/3D/1370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(Cl)C=C1C) `REAL300000300933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300933 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 9, 13, 13, 13, 13, 13, 9, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 9, 2, 2, 2, 1, 1, 2, 2, 2] 13 rigid atoms, others: [33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 71 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300933 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 48 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300933 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300933 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300933/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300933 Building REAL300000300934 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300934' /scratch/stefan/7770550/working/building/REAL300000300934 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300934 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300934/0 /scratch/stefan/7770550/working/building/REAL300000300934 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1371) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1371 `/scratch/stefan/7770550/working/3D/1371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300934 none COC1=NSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 43, 43, 43, 43, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 43, 47, 47, 47, 1, 1, 1, 2, 2, 2, 43] 47 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18, 19, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300934 none COC1=NSC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 43, 43, 23, 23, 43, 43, 43, 43, 43, 1, 3, 3, 3, 43, 43, 43, 43, 43, 43, 1] 47 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300934 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300934 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300934/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300934 Building REAL300000300935 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300935' /scratch/stefan/7770550/working/building/REAL300000300935 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300935 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300935/0 /scratch/stefan/7770550/working/building/REAL300000300935 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1372) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1372 `/scratch/stefan/7770550/working/3D/1372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300935 none COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [30, 27, 27, 27, 27, 27, 27, 64, 64, 64, 64, 27, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 30, 30, 30, 27, 27, 64, 64, 64, 64, 64, 64, 27, 1, 1, 1, 2, 2, 2] 64 rigid atoms, others: [39, 40, 41, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 197 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300935 none COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 17, 27, 27, 17, 17, 27, 27, 27, 27, 27, 4, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 1, 27, 27, 27, 27, 27, 27] 64 rigid atoms, others: [1, 2, 3, 4, 5, 6, 11, 12, 13, 38, 30, 31] set([0, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300935 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300935/1 /scratch/stefan/7770550/working/building/REAL300000300935 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1373) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1373 `/scratch/stefan/7770550/working/3D/1373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300935.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300935 none COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 21, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 5, 1, 1, 1, 2, 2, 2] 50 rigid atoms, others: [40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45]) total number of confs: 155 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300935 none COC1=CC=C(C(=O)N(C)C)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 15, 21, 21, 15, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 1, 15, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 38, 30, 31] set([7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300935 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300935 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300935/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300935/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300935 Building REAL300000300936 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300936' /scratch/stefan/7770550/working/building/REAL300000300936 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300936 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300936/0 /scratch/stefan/7770550/working/building/REAL300000300936 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1374) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1374 `/scratch/stefan/7770550/working/3D/1374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CC1CCCC(C)(C)O1) `REAL300000300936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300936 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CC1CCCC(C)(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 52, 52, 68, 68, 68, 68, 52, 25, 7, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 52, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1] 68 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300936 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)CC1CCCC(C)(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 53, 68, 68, 68, 68, 68, 68, 68, 2, 2, 2, 1, 1, 1, 7, 53, 53, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300936 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300936 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300936/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300936 Building REAL300000300937 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300937' /scratch/stefan/7770550/working/building/REAL300000300937 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300937 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300937/0 /scratch/stefan/7770550/working/building/REAL300000300937 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1375) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1375 `/scratch/stefan/7770550/working/3D/1375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C=CC1=CC=CC=C1Cl) `REAL300000300937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300937 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C=CC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 124, 139, 159, 159, 159, 159, 124, 65, 9, 65, 65, 9, 1, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 159, 124, 9, 9, 1, 1, 1, 1] 159 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 668 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300937 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C=CC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 21, 106, 106, 159, 159, 106, 159, 159, 159, 2, 2, 2, 1, 1, 1, 8, 106, 106, 159, 159, 159, 159] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 620 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300937 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300937 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300937/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300937 Building REAL300000300938 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300938' /scratch/stefan/7770550/working/building/REAL300000300938 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300938 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300938/0 /scratch/stefan/7770550/working/building/REAL300000300938 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1376) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1376 `/scratch/stefan/7770550/working/3D/1376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300938 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 36, 36, 36, 36, 36, 36, 1, 1, 1, 2, 2, 2] 36 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300938 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 36, 36, 23, 27, 36, 36, 36, 36, 36, 4, 4, 4, 1, 1, 1, 36, 36, 36, 36, 36, 36] 36 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300938 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300938/1 /scratch/stefan/7770550/working/building/REAL300000300938 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1377) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1377 `/scratch/stefan/7770550/working/3D/1377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300938.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300938/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300938 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 28, 31, 31, 31, 31, 31, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 7, 1, 1, 1, 2, 2, 2] 31 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300938 none COC1=CC(C(=O)[O-])=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 31, 31, 27, 31, 31, 31, 31, 31, 31, 4, 4, 4, 1, 1, 1, 17, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300938 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300938 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300938/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300938/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300938 Building REAL300000300939 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300939' /scratch/stefan/7770550/working/building/REAL300000300939 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300939 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300939/0 /scratch/stefan/7770550/working/building/REAL300000300939 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1378) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1378 `/scratch/stefan/7770550/working/3D/1378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(C(N)=O)O1) `REAL300000300939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300939 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 59, 59, 37, 37, 37, 37, 1, 1, 1, 2, 2, 2, 37, 59, 59] 59 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 32, 34, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 29, 30, 31]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300939 none CC1=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C(C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 17, 37, 37, 23, 27, 37, 37, 37, 37, 37, 1, 1, 1, 4, 4, 1, 2, 2, 2, 37, 37, 37, 37, 37, 37, 1, 5, 5] 59 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300939 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300939/1 /scratch/stefan/7770550/working/building/REAL300000300939 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1379) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1379 `/scratch/stefan/7770550/working/3D/1379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(C(N)=O)O1) `REAL300000300939.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300939 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 31, 31, 31, 47, 47, 31, 31, 31, 31, 8, 1, 1, 1, 2, 2, 2, 31, 47, 47] 47 rigid atoms, others: [6, 7, 8, 9, 10, 11, 14, 15, 16, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300939 none CC1=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C(C(N)=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 8, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 11, 31, 31, 11, 17, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 1, 2, 2, 2, 11, 31, 31, 31, 31, 31, 31, 1, 5, 5] 47 rigid atoms, others: [0, 1, 2, 3, 33, 17, 18, 19, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300939 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300939 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300939/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300939/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300939 Building REAL300000300940 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300940' /scratch/stefan/7770550/working/building/REAL300000300940 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300940 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300940/0 /scratch/stefan/7770550/working/building/REAL300000300940 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1380) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1380 `/scratch/stefan/7770550/working/3D/1380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300940 none CCCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 32, 32, 32, 32, 32, 32, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 7, 1, 1, 1, 2, 2, 2] 45 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 171 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300940 none CCCC1=CC=CC=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 32, 32, 18, 22, 32, 32, 32, 32, 32, 9, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 13, 32, 32, 32, 32, 32, 32] 45 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300940 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300940 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300940/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300940 Building REAL300000300941 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300941' /scratch/stefan/7770550/working/building/REAL300000300941 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300941 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300941/0 /scratch/stefan/7770550/working/building/REAL300000300941 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1381) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1381 `/scratch/stefan/7770550/working/3D/1381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC=C1C(F)F) `REAL300000300941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300941 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 21, 21, 45, 45, 45, 45, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 5, 5, 45, 45, 45, 45, 45, 45, 1, 1, 5] 45 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300941 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 45, 45, 45, 45, 45, 45, 45, 2, 2, 2, 1, 1, 1, 45, 45, 45] 45 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300941 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300941/1 /scratch/stefan/7770550/working/building/REAL300000300941 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1382) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1382 `/scratch/stefan/7770550/working/3D/1382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC=C1C(F)F) `REAL300000300941.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300941 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 13, 23, 31, 31, 31, 31, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 8, 8, 31, 31, 31, 31, 31, 31, 13, 1, 1, 8] 39 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300941 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CSC=C1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 5, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 17, 17, 17, 31, 31, 31, 31, 31, 39, 39, 2, 2, 2, 1, 1, 1, 7, 31, 31, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300941 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300941 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300941/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300941/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300941 Building REAL300000300942 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300942' /scratch/stefan/7770550/working/building/REAL300000300942 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300942 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300942/0 /scratch/stefan/7770550/working/building/REAL300000300942 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1383) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1383 `/scratch/stefan/7770550/working/3D/1383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1) `REAL300000300942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300942 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 15, 15, 25, 25, 25, 25, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 25, 25, 25, 25, 25, 1] 25 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300942 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300942 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300942 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300942/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300942 Building REAL300000300943 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300943' /scratch/stefan/7770550/working/building/REAL300000300943 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300943 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300943/0 /scratch/stefan/7770550/working/building/REAL300000300943 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1384) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1384 `/scratch/stefan/7770550/working/3D/1384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300943 none CC1=NN(CC2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 68, 68, 68, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 16, 16, 16, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 36, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 474 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300943 none CC1=NN(CC2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 16, 16, 10, 16, 16, 1, 1, 1, 1, 10, 10, 10, 23, 39, 39, 35, 36, 39, 39, 39, 39, 39, 2, 2, 2, 8, 8, 16, 16, 16, 16, 16, 2, 2, 2, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 14] set([5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300943 none CC1=NN(CC2=CC=CC=C2)C(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 181, 201, 201, 201, 201, 201, 39, 39, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 181, 181, 201, 201, 201, 201, 201, 39, 39, 39, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [41, 42, 43, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 664 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300943 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300943 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300943/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300943 Building REAL300000300944 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300944' /scratch/stefan/7770550/working/building/REAL300000300944 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300944 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300944/0 /scratch/stefan/7770550/working/building/REAL300000300944 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1385) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1385 `/scratch/stefan/7770550/working/3D/1385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=NC=C21) `REAL300000300944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300944 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=NC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300944 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=CC=NC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300944 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300944/1 /scratch/stefan/7770550/working/building/REAL300000300944 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1386) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1386 `/scratch/stefan/7770550/working/3D/1386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=NC=C21) `REAL300000300944.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300944 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=NC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300944 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=CC=NC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300944 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300944 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300944/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300944/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300944 Building REAL300000300945 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300945' /scratch/stefan/7770550/working/building/REAL300000300945 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300945 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300945/0 /scratch/stefan/7770550/working/building/REAL300000300945 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1387) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1387 `/scratch/stefan/7770550/working/3D/1387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CN(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300945 none COC(=O)C1=CN(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 25, 58, 25, 25, 25, 25, 13, 6, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 58, 58, 58, 25, 25, 25, 25, 1, 1, 1, 2, 2, 2, 25] 58 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300945 none COC(=O)C1=CN(C)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 25, 25, 15, 19, 25, 25, 25, 25, 25, 1, 10, 10, 10, 1, 2, 2, 2, 25, 25, 25, 25, 25, 25, 1] 58 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 23, 27, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300945 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300945/1 /scratch/stefan/7770550/working/building/REAL300000300945 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1388) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1388 `/scratch/stefan/7770550/working/3D/1388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CN(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300945.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300945 none COC(=O)C1=CN(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 30, 68, 30, 30, 30, 30, 15, 8, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 68, 68, 68, 30, 30, 30, 30, 8, 1, 1, 1, 2, 2, 2, 30] 68 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300945 none COC(=O)C1=CN(C)C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 30, 30, 17, 26, 30, 30, 30, 30, 30, 1, 11, 11, 11, 1, 2, 2, 2, 17, 30, 30, 30, 30, 30, 30, 1] 68 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 38, 23, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300945 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300945 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300945/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300945/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300945 Building REAL300000300946 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300946' /scratch/stefan/7770550/working/building/REAL300000300946 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300946 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300946/0 /scratch/stefan/7770550/working/building/REAL300000300946 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1389) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1389 `/scratch/stefan/7770550/working/3D/1389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C#N)=C1F) `REAL300000300946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300946 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C#N)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 17, 22, 25, 25, 25, 25, 17, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 1, 1, 1] 25 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300946 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC(C#N)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300946 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300946 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300946/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300946 Building REAL300000300947 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300947' /scratch/stefan/7770550/working/building/REAL300000300947 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300947 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300947/0 /scratch/stefan/7770550/working/building/REAL300000300947 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1390) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1390 `/scratch/stefan/7770550/working/3D/1390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=C(Cl)OC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1) `REAL300000300947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300947 none COC(=O)C1=C(Cl)OC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 16, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 53, 75, 53, 53, 53, 53, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 75, 75, 75, 1, 1, 1, 2, 2, 2, 53] 75 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 32, 23, 24, 25, 26, 30, 31]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300947 none COC(=O)C1=C(Cl)OC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 16, 12, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 53, 53, 25, 43, 53, 53, 53, 53, 53, 1, 5, 5, 5, 53, 53, 53, 53, 53, 53, 1] 75 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 23] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300947 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300947 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300947/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300947 Building REAL300000300948 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300948' /scratch/stefan/7770550/working/building/REAL300000300948 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300948 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300948/0 /scratch/stefan/7770550/working/building/REAL300000300948 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1391) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1391 `/scratch/stefan/7770550/working/3D/1391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CC(C)(C)C2=C1) `REAL300000300948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300948 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CC(C)(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1] 17 rigid atoms, others: [34, 35, 36, 37, 38, 11, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300948 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)CC(C)(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300948 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300948 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300948/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300948 Building REAL300000300949 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300949' /scratch/stefan/7770550/working/building/REAL300000300949 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300949 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300949/0 /scratch/stefan/7770550/working/building/REAL300000300949 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1392) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1392 `/scratch/stefan/7770550/working/3D/1392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21) `REAL300000300949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300949 none CCC(=O)N1CCC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 65, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 65, 65, 65, 65, 65, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 65 rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300949 none CCC(=O)N1CCC2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 65 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 34, 45, 25, 36, 26, 37] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300949 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300949/1 /scratch/stefan/7770550/working/building/REAL300000300949 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1393) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1393 `/scratch/stefan/7770550/working/3D/1393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21) `REAL300000300949.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300949 none CCC(=O)N1CCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 17, 48, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 48, 48, 48, 48, 48, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 48 rigid atoms, others: [38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300949 none CCC(=O)N1CCC2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 12, 17, 17, 17, 17, 17, 17, 1, 1, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1] 48 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 10, 11, 44, 34, 25, 36, 26, 37] set([0, 1, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300949 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300949 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300949/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300949/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300949 Building REAL300000300950 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300950' /scratch/stefan/7770550/working/building/REAL300000300950 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300950 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300950/0 /scratch/stefan/7770550/working/building/REAL300000300950 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1394) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1394 `/scratch/stefan/7770550/working/3D/1394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCC2)N=C1) `REAL300000300950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300950 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 9, 17, 27, 27, 27, 27, 9, 2, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 1, 1, 27, 27, 27, 27, 27, 27, 1, 7, 7, 7, 7, 7, 7, 7, 1] 63 rigid atoms, others: [37, 11, 14, 15, 16, 17, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300950 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 27, 27, 27, 63, 63, 63, 27, 27, 2, 2, 2, 1, 1, 1, 27, 63, 63, 63, 63, 63, 63, 63, 27] 63 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300950 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C2CCC2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 37, 63, 63, 63, 63, 63, 37, 13, 7, 13, 13, 7, 7, 1, 1, 1, 1, 1, 7, 7, 63, 63, 63, 63, 63, 63, 7, 1, 1, 1, 1, 1, 1, 1, 7] 63 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 260 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300950 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300950 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300950/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300950 Building REAL300000300951 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300951' /scratch/stefan/7770550/working/building/REAL300000300951 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300951 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300951/0 /scratch/stefan/7770550/working/building/REAL300000300951 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1395) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1395 `/scratch/stefan/7770550/working/3D/1395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1C1CCC1) `REAL300000300951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300951 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 29, 45, 50, 50, 50, 50, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 50, 1, 1, 6, 6, 6, 6, 6, 6, 6] 59 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 194 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300951 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 17, 17, 17, 50, 50, 50, 50, 50, 59, 59, 59, 2, 2, 2, 1, 1, 1, 50, 50, 59, 59, 59, 59, 59, 59, 59] 59 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300951 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 48, 59, 59, 59, 59, 59, 40, 20, 6, 20, 20, 6, 6, 6, 6, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 6, 6, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [32, 33, 34, 35, 36, 37, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 181 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300951 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300951 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300951/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300951 Building REAL300000300952 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300952' /scratch/stefan/7770550/working/building/REAL300000300952 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300952 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300952/0 /scratch/stefan/7770550/working/building/REAL300000300952 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1396) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1396 `/scratch/stefan/7770550/working/3D/1396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1CC1CCC1) `REAL300000300952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300952 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [62, 62, 62, 23, 23, 62, 62, 62, 62, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 62, 62, 62, 62, 62, 62, 1, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21] 152 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 353 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300952 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 62, 62, 62, 62, 62, 119, 152, 152, 152, 2, 2, 2, 1, 1, 1, 62, 62, 119, 119, 152, 152, 152, 152, 152, 152, 152] 152 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 550 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300952 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 105, 105, 152, 152, 152, 152, 105, 52, 21, 52, 52, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 152, 152, 152, 152, 152, 152, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1] 152 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 679 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300952 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300952/1 /scratch/stefan/7770550/working/building/REAL300000300952 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1397) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1397 `/scratch/stefan/7770550/working/3D/1397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=NN1CC1CCC1) `REAL300000300952.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300952 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 25, 45, 64, 64, 64, 64, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 64, 64, 64, 64, 64, 64, 25, 1, 1, 6, 6, 21, 21, 21, 21, 21, 21, 21] 151 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 378 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300952 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 19, 19, 19, 64, 64, 64, 64, 64, 130, 151, 151, 151, 2, 2, 2, 1, 1, 1, 7, 64, 64, 130, 130, 151, 151, 151, 151, 151, 151, 151] 151 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 559 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: REAL300000300952 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=NN1CC1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 112, 151, 151, 151, 151, 151, 112, 58, 21, 58, 58, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 151, 112, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1] 151 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 621 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300952 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300952 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300952/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300952/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300952 Building REAL300000300953 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300953' /scratch/stefan/7770550/working/building/REAL300000300953 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300953 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300953/0 /scratch/stefan/7770550/working/building/REAL300000300953 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1398) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1398 `/scratch/stefan/7770550/working/3D/1398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12) `REAL300000300953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300953 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 23, 35, 23, 23, 23, 19, 7, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 35, 35, 35, 23, 23, 1, 1, 1, 2, 2, 2, 23, 23, 23, 23] 35 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300953 none COC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 5, 9, 23, 23, 9, 13, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1] 35 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 41, 42, 39, 40, 22, 23, 24, 25, 26, 27, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300953 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300953/1 /scratch/stefan/7770550/working/building/REAL300000300953 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1399) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1399 `/scratch/stefan/7770550/working/3D/1399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12) `REAL300000300953.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300953 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 19, 33, 19, 19, 19, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 33, 33, 33, 19, 19, 7, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19] 33 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300953 none COC(=O)C1=CC=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 3, 7, 19, 19, 7, 11, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 7, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1] 33 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 41, 42, 43, 40, 22, 23, 24, 25, 26, 27, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300953 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300953 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300953/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300953/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300953 Building REAL300000300954 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300954' /scratch/stefan/7770550/working/building/REAL300000300954 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300954 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300954/0 /scratch/stefan/7770550/working/building/REAL300000300954 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1400) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1400 `/scratch/stefan/7770550/working/3D/1400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300954 none CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [53, 34, 13, 13, 13, 13, 13, 13, 51, 51, 51, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 53, 53, 53, 53, 53, 13, 13, 51, 51, 51, 13, 1, 1, 1, 2, 2, 2] 71 rigid atoms, others: [38, 39, 40, 16, 17, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300954 none CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 1, 7, 7, 7, 7, 13, 13, 7, 13, 13, 13, 13, 13, 13, 17, 17, 17, 17, 17, 1, 1, 10, 10, 10, 1, 13, 13, 13, 13, 13, 13] 71 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 11, 12, 13, 37] set([0, 1, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300954 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300954/1 /scratch/stefan/7770550/working/building/REAL300000300954 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1401) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1401 `/scratch/stefan/7770550/working/3D/1401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300954.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300954 none CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [53, 37, 17, 17, 17, 17, 17, 17, 55, 55, 55, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 17, 17, 55, 55, 55, 17, 5, 1, 1, 1, 2, 2, 2] 70 rigid atoms, others: [39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300954 none CCOC1=CC=C(C(=O)OC)C=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [11, 6, 1, 1, 1, 1, 1, 1, 12, 12, 12, 1, 1, 1, 7, 7, 7, 9, 17, 17, 13, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11, 1, 1, 13, 13, 13, 1, 9, 17, 17, 17, 17, 17, 17] 70 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 11, 12, 13, 37] set([0, 1, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300954 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300954 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300954/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300954/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300954 Building REAL300000300955 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300955' /scratch/stefan/7770550/working/building/REAL300000300955 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300955 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300955/0 /scratch/stefan/7770550/working/building/REAL300000300955 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1402) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1402 `/scratch/stefan/7770550/working/3D/1402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(O)C=CC=C1OC(F)(F)F) `REAL300000300955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300955 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(O)C=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 1, 1] 8 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300955 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(O)C=CC=C1OC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 8, 4, 4, 4] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 24 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300955 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300955 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300955/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300955 Building REAL300000300956 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300956' /scratch/stefan/7770550/working/building/REAL300000300956 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300956 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300956/0 /scratch/stefan/7770550/working/building/REAL300000300956 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1403) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1403 `/scratch/stefan/7770550/working/3D/1403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2OCC(C)(C)CN2N=C1) `REAL300000300956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300956 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2OCC(C)(C)CN2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 5, 5, 5, 5, 5, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 19, 34, 34, 34, 34, 34, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1] 34 rigid atoms, others: [32, 39, 40, 41, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300956 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2OCC(C)(C)CN2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 5, 5, 5, 5, 5, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 2, 2, 2, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300956 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300956 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300956/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300956 Building REAL300000300957 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300957' /scratch/stefan/7770550/working/building/REAL300000300957 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300957 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300957/0 /scratch/stefan/7770550/working/building/REAL300000300957 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1404) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1404 `/scratch/stefan/7770550/working/3D/1404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2=CC=CC=C2)S1) `REAL300000300957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300957 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 23, 23, 31, 31, 31, 31, 23, 6, 1, 6, 6, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 31, 31, 31, 31, 31, 31, 1, 4, 4, 2, 4, 4] 31 rigid atoms, others: [11, 14, 15, 16, 17, 18, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300957 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 31, 31, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300957 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 27, 27, 31, 31, 31, 31, 27, 15, 4, 15, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 31, 31, 31, 31, 31, 31, 4, 1, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 34, 35, 36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 105 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300957 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300957 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300957/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300957 Building REAL300000300958 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300958' /scratch/stefan/7770550/working/building/REAL300000300958 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300958 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300958/0 /scratch/stefan/7770550/working/building/REAL300000300958 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1405) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1405 `/scratch/stefan/7770550/working/3D/1405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)COC2=C1) `REAL300000300958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300958 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)COC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300958 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2NC(=O)COC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300958 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300958/1 /scratch/stefan/7770550/working/building/REAL300000300958 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1406) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1406 `/scratch/stefan/7770550/working/3D/1406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)COC2=C1) `REAL300000300958.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300958 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)COC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 14, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300958 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C2NC(=O)COC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300958 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300958 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300958/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300958/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300958 Building REAL300000300959 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300959' /scratch/stefan/7770550/working/building/REAL300000300959 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300959 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300959/0 /scratch/stefan/7770550/working/building/REAL300000300959 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1407) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1407 `/scratch/stefan/7770550/working/3D/1407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)C=CO1) `REAL300000300959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300959 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 33, 33, 53, 53, 53, 53, 33, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 1, 1] 53 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300959 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Br)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 17, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 53, 53, 53, 53, 53, 2, 2, 2, 1, 1, 1, 53, 53] 53 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300959 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300959 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300959/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300959 Building REAL300000300960 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300960' /scratch/stefan/7770550/working/building/REAL300000300960 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300960 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300960/0 /scratch/stefan/7770550/working/building/REAL300000300960 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1408) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1408 `/scratch/stefan/7770550/working/3D/1408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300960 none COC1=C(F)C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 5, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 2, 2, 2, 11] 11 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300960 none COC1=C(F)C=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 5, 5, 11, 11, 11, 11, 11, 1, 1, 1, 5, 5, 5, 1, 5, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 35, 21, 22, 23, 27] set([0, 32, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300960 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300960/1 /scratch/stefan/7770550/working/building/REAL300000300960 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1409) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1409 `/scratch/stefan/7770550/working/3D/1409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300960.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300960 none COC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 2, 13] 13 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300960 none COC1=C(F)C=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 5, 5, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 1, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 21, 22, 23, 27] set([0, 32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300960 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300960 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300960/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300960/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300960 Building REAL300000300961 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300961' /scratch/stefan/7770550/working/building/REAL300000300961 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300961 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300961/0 /scratch/stefan/7770550/working/building/REAL300000300961 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1410) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1410 `/scratch/stefan/7770550/working/3D/1410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2CCCCN12) `REAL300000300961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300961 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2CCCCN12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 18, 23, 23, 23, 23, 23, 16, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300961 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2CCCCN12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300961 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300961/1 /scratch/stefan/7770550/working/building/REAL300000300961 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1411) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1411 `/scratch/stefan/7770550/working/3D/1411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2CCCCN12) `REAL300000300961.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300961 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2CCCCN12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 15, 22, 22, 22, 22, 22, 15, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300961 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=C2CCCCN12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 1, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300961 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300961 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300961/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300961/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300961 Building REAL300000300962 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300962' /scratch/stefan/7770550/working/building/REAL300000300962 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300962 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300962/0 /scratch/stefan/7770550/working/building/REAL300000300962 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1412) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1412 `/scratch/stefan/7770550/working/3D/1412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300962 none COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 27, 27, 53, 53, 53, 17, 7, 17, 17, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 2, 2, 2, 53] 53 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 204 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300962 none COC1=CC(F)=C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 53, 53, 25, 25, 53, 53, 53, 53, 53, 1, 1, 1, 4, 4, 4, 1, 53, 53, 53, 53, 53, 53, 1] 53 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300962 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300962/1 /scratch/stefan/7770550/working/building/REAL300000300962 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1413) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1413 `/scratch/stefan/7770550/working/3D/1413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F) `REAL300000300962.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300962 none COC1=CC(F)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 23, 23, 49, 49, 49, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 5, 1, 1, 1, 2, 2, 2, 49] 49 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300962 none COC1=CC(F)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 49, 49, 32, 45, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 4, 1, 25, 49, 49, 49, 49, 49, 49, 1] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 21, 22, 23, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300962 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300962 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300962/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300962/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300962 Building REAL300000300963 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300963' /scratch/stefan/7770550/working/building/REAL300000300963 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300963 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300963/0 /scratch/stefan/7770550/working/building/REAL300000300963 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1414) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1414 `/scratch/stefan/7770550/working/3D/1414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(C)C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300000300963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300963 none COC1=CC(C(C)C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17] 17 rigid atoms, others: [38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300963 none COC1=CC(C(C)C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 5, 17, 17, 5, 9, 17, 17, 17, 17, 17, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 5, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2] 17 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 44, 23, 24, 25, 29] set([0, 6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300963 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300963 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300963/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300963 Building REAL300000300964 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300964' /scratch/stefan/7770550/working/building/REAL300000300964 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300964 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300964/0 /scratch/stefan/7770550/working/building/REAL300000300964 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1415) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1415 `/scratch/stefan/7770550/working/3D/1415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1OC(C)C) `REAL300000300964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300964 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 23, 23, 57, 57, 57, 57, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 57, 57, 57, 57, 57, 57, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19] 96 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 342 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300964 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(F)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 57, 57, 57, 27, 57, 57, 57, 94, 96, 96, 2, 2, 2, 1, 1, 1, 57, 27, 57, 96, 96, 96, 96, 96, 96, 96] 96 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 264 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300964 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300964/1 /scratch/stefan/7770550/working/building/REAL300000300964 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1416) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1416 `/scratch/stefan/7770550/working/3D/1416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1OC(C)C) `REAL300000300964.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300964/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300964 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 25, 44, 52, 52, 52, 52, 25, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 52, 52, 52, 52, 52, 52, 25, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18] 89 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 308 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300964 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(F)=CC=C1OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 15, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 16, 16, 16, 52, 52, 52, 25, 52, 52, 52, 89, 89, 89, 2, 2, 2, 1, 1, 1, 7, 52, 25, 52, 89, 89, 89, 89, 89, 89, 89] 89 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 241 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300964 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300964 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300964/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300964/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300964 Building REAL300000300965 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300965' /scratch/stefan/7770550/working/building/REAL300000300965 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300965 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300965/0 /scratch/stefan/7770550/working/building/REAL300000300965 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1417) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1417 `/scratch/stefan/7770550/working/3D/1417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C) `REAL300000300965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300965 none CC1=CSC(C)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 13, 7, 13, 13, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 7, 1, 1, 1, 2, 2, 2] 22 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300965 none CC1=CSC(C)=C1S(=O)(=O)NC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 15, 22, 22, 15, 15, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 2, 2, 15, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300965 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300965/1 /scratch/stefan/7770550/working/building/REAL300000300965 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1418) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1418 `/scratch/stefan/7770550/working/3D/1418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300965.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300965 none CC1=CSC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 14, 7, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 2] 23 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300965 none CC1=CSC(C)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 23, 23, 15, 15, 23, 23, 23, 23, 23, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300965 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300965 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300965/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300965/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300965 Building REAL300000300966 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300966' /scratch/stefan/7770550/working/building/REAL300000300966 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300966 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300966/0 /scratch/stefan/7770550/working/building/REAL300000300966 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1419) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1419 `/scratch/stefan/7770550/working/3D/1419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OC(C)C2) `REAL300000300966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300966 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 21, 21, 35, 35, 35, 35, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 2, 2, 2, 1, 1] 35 rigid atoms, others: [32, 33, 37, 38, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300966 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=CC2=C1OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 35, 35, 2, 2, 2, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300966 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300966/1 /scratch/stefan/7770550/working/building/REAL300000300966 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1420) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1420 `/scratch/stefan/7770550/working/3D/1420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OC(C)C2) `REAL300000300966.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300966 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 21, 37, 37, 37, 37, 37, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 21, 1, 1, 1, 1, 2, 2, 2, 1, 1] 37 rigid atoms, others: [32, 33, 34, 38, 39, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 172 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300966 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=CC2=C1OC(C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 37, 37, 2, 2, 2, 1, 1, 1, 7, 37, 37, 37, 37, 37, 37, 37, 37, 37] 37 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300966 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300966 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300966/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300966/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300966 Building REAL300000300967 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300967' /scratch/stefan/7770550/working/building/REAL300000300967 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300967 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300967/0 /scratch/stefan/7770550/working/building/REAL300000300967 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1421) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1421 `/scratch/stefan/7770550/working/3D/1421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C(C)(C)C)S1) `REAL300000300967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300967 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 13, 21, 21, 21, 21, 21, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 4, 4, 4, 1, 21, 21, 21, 21, 21, 21, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 37 rigid atoms, others: [11, 14, 15, 16, 17, 18, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300967 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C(C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 21, 21, 21, 21, 37, 37, 37, 21, 2, 2, 2, 1, 1, 1, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300967 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300967 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300967/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300967 Building REAL300000300968 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300968' /scratch/stefan/7770550/working/building/REAL300000300968 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300968 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300968/0 /scratch/stefan/7770550/working/building/REAL300000300968 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1422) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1422 `/scratch/stefan/7770550/working/3D/1422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2(C#N)CC2)C=C1) `REAL300000300968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300968 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2(C#N)CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 9, 5, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 6, 6, 6, 6, 1, 1] 23 rigid atoms, others: [32, 33, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 51 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300968 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2(C#N)CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 23, 23, 23, 23, 9, 9] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300968 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(C2(C#N)CC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 13, 23, 23, 23, 23, 23, 13, 6, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 23, 13, 6, 6, 1, 1, 1, 1, 6, 6] 23 rigid atoms, others: [34, 35, 36, 37, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 122 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300968 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300968 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300968/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300968 Building REAL300000300969 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300969' /scratch/stefan/7770550/working/building/REAL300000300969 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300969 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300969/0 /scratch/stefan/7770550/working/building/REAL300000300969 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1423) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1423 `/scratch/stefan/7770550/working/3D/1423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300969 none COC1=C(F)C=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 68, 68, 68, 68, 68, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 68, 68, 68, 68, 68, 1, 1, 1, 2, 2, 2] 68 rigid atoms, others: [13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300969 none COC1=C(F)C=CC(F)=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 26, 68, 68, 26, 26, 68, 68, 68, 68, 68, 7, 7, 7, 1, 1, 68, 68, 68, 68, 68, 68] 68 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300969 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300969 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300969/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300969 Building REAL300000300970 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300970' /scratch/stefan/7770550/working/building/REAL300000300970 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300970 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300970/0 /scratch/stefan/7770550/working/building/REAL300000300970 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1424) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1424 `/scratch/stefan/7770550/working/3D/1424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC2=C1OCCO2) `REAL300000300970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300970 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 25, 40, 40, 40, 40, 40, 25, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [32, 33, 34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 25, 26, 27, 28, 29, 30]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300970 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)C=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 2, 2, 2, 1, 1, 1, 40, 40, 40, 40, 40, 40] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300970 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300970 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300970/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300970 Building REAL300000300971 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300971' /scratch/stefan/7770550/working/building/REAL300000300971 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300971 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300971/0 /scratch/stefan/7770550/working/building/REAL300000300971 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1425) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1425 `/scratch/stefan/7770550/working/3D/1425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21) `REAL300000300971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300971 none CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 19, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 19, 19, 19, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17] 19 rigid atoms, others: [39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300971 none CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)NC3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 9, 17, 17, 17, 17, 17, 17, 1, 1, 4, 4, 4, 1, 1, 1, 2, 2, 2, 1, 1, 9, 17, 17, 17, 17, 17, 17, 1] 19 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 45, 25, 36, 26, 37, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 95 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300971 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300971/1 /scratch/stefan/7770550/working/building/REAL300000300971 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1426) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1426 `/scratch/stefan/7770550/working/3D/1426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21) `REAL300000300971.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300971 none CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 33, 17, 17, 17, 17, 17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 33, 33, 33, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17] 33 rigid atoms, others: [38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 116 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300971 none CC(=O)N1CC(C)C2=CC=C(S(=O)(=O)[N-]C3=CC=C(C(=O)[O-])C=C3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17, 1] 33 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 44, 25, 36, 26, 37, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 50 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300971 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300971 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300971/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300971/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300971 Building REAL300000300972 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300972' /scratch/stefan/7770550/working/building/REAL300000300972 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300972 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300972/0 /scratch/stefan/7770550/working/building/REAL300000300972 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1427) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1427 `/scratch/stefan/7770550/working/3D/1427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC=C1Cl) `REAL300000300972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300972 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 9, 17, 19, 19, 19, 19, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300972 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CSC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 14, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300972 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300972 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300972/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300972 Building REAL300000300973 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300973' /scratch/stefan/7770550/working/building/REAL300000300973 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300973 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300973/0 /scratch/stefan/7770550/working/building/REAL300000300973 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1428) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1428 `/scratch/stefan/7770550/working/3D/1428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Br)=NN1C) `REAL300000300973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300973 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Br)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 17, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 13, 13, 20, 20, 20, 20, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2] 20 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300973 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(Br)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Br', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 17, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 20, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300973 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300973 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300973/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300973 Building REAL300000300974 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300974' /scratch/stefan/7770550/working/building/REAL300000300974 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300974 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300974/0 /scratch/stefan/7770550/working/building/REAL300000300974 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1429) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1429 `/scratch/stefan/7770550/working/3D/1429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(C(F)(F)F)=C1) `REAL300000300974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300974 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300974 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300974 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300974/1 /scratch/stefan/7770550/working/building/REAL300000300974 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1430) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1430 `/scratch/stefan/7770550/working/3D/1430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(C(F)(F)F)=C1) `REAL300000300974.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300974 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 9, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300974 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CN=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300974 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300974 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300974/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300974/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300974 Building REAL300000300975 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300975' /scratch/stefan/7770550/working/building/REAL300000300975 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300975 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300975/0 /scratch/stefan/7770550/working/building/REAL300000300975 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1431) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1431 `/scratch/stefan/7770550/working/3D/1431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN2C=CC=NC2=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300975 none CC1=NN2C=CC=NC2=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 49, 49, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 1, 1, 1, 2, 2, 2] 49 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300975 none CC1=NN2C=CC=NC2=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 8, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 1, 12, 12, 12, 30, 49, 49, 30, 49, 49, 49, 49, 49, 49, 2, 2, 2, 1, 1, 1, 49, 49, 49, 49, 49, 49] 49 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300975 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300975 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300975/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300975 Building REAL300000300976 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300976' /scratch/stefan/7770550/working/building/REAL300000300976 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300976 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300976/0 /scratch/stefan/7770550/working/building/REAL300000300976 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1432) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1432 `/scratch/stefan/7770550/working/3D/1432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=NON=C2C=C1) `REAL300000300976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300976 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=NON=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300976 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=NON=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300976 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300976/1 /scratch/stefan/7770550/working/building/REAL300000300976 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1433) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1433 `/scratch/stefan/7770550/working/3D/1433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=NON=C2C=C1) `REAL300000300976.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300976 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=NON=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300976 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=NON=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 8, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300976 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300976 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300976/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300976/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300976 Building REAL300000300977 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300977' /scratch/stefan/7770550/working/building/REAL300000300977 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300977 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300977/0 /scratch/stefan/7770550/working/building/REAL300000300977 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1434) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1434 `/scratch/stefan/7770550/working/3D/1434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2S1) `REAL300000300977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300977 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300977 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC2=CC=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300977 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300977 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300977/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300977 Building REAL300000300978 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300978' /scratch/stefan/7770550/working/building/REAL300000300978 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300978 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300978/0 /scratch/stefan/7770550/working/building/REAL300000300978 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1435) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1435 `/scratch/stefan/7770550/working/3D/1435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2NC=C(Cl)C=C12) `REAL300000300978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300978 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2NC=C(Cl)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 24, 33, 33, 33, 33, 33, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300978 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN=C2NC=C(Cl)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 1, 8, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300978 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300978 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300978/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300978 Building REAL300000300979 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300979' /scratch/stefan/7770550/working/building/REAL300000300979 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300979 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300979/0 /scratch/stefan/7770550/working/building/REAL300000300979 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1436) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1436 `/scratch/stefan/7770550/working/3D/1436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C2CC2)=NN1C) `REAL300000300979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300979 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C2CC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [45, 45, 45, 21, 21, 45, 45, 45, 45, 21, 7, 1, 7, 7, 1, 1, 1, 1, 12, 12, 1, 1, 1, 45, 45, 45, 45, 45, 45, 1, 12, 12, 12, 12, 12, 2, 2, 2] 82 rigid atoms, others: [11, 14, 15, 16, 17, 20, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 243 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300979 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C2CC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 45, 45, 45, 82, 82, 45, 45, 45, 2, 2, 2, 1, 1, 1, 45, 82, 82, 82, 82, 82, 45, 45, 45] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 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: REAL300000300979 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC(C2CC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 67, 67, 82, 82, 82, 82, 67, 38, 12, 38, 38, 12, 12, 1, 1, 1, 1, 12, 12, 12, 82, 82, 82, 82, 82, 82, 12, 1, 1, 1, 1, 1, 12, 12, 12] 82 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 303 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300979 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300979/1 /scratch/stefan/7770550/working/building/REAL300000300979 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1437) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1437 `/scratch/stefan/7770550/working/3D/1437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C2CC2)=NN1C) `REAL300000300979.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300979 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C2CC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 22, 22, 46, 46, 46, 46, 22, 6, 1, 6, 6, 1, 1, 1, 1, 12, 12, 1, 1, 1, 46, 46, 46, 46, 46, 46, 22, 1, 12, 12, 12, 12, 12, 2, 2, 2] 80 rigid atoms, others: [11, 14, 15, 16, 17, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 264 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300979 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C2CC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 46, 46, 46, 80, 80, 46, 46, 46, 2, 2, 2, 1, 1, 1, 7, 46, 80, 80, 80, 80, 80, 46, 46, 46] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 247 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300979 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C2CC2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 74, 74, 80, 80, 80, 80, 74, 38, 12, 38, 38, 12, 12, 1, 1, 1, 1, 12, 12, 12, 80, 80, 80, 80, 80, 80, 74, 12, 1, 1, 1, 1, 1, 12, 12, 12] 80 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 283 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300979 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300979 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300979/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300979/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300979 Building REAL300000300980 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300980' /scratch/stefan/7770550/working/building/REAL300000300980 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300980 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300980/0 /scratch/stefan/7770550/working/building/REAL300000300980 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1438) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1438 `/scratch/stefan/7770550/working/3D/1438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(C)C(F)=C1C) `REAL300000300980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300980 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(C)C(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 5, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 15, 15, 23, 23, 23, 23, 15, 11, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 15, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2] 23 rigid atoms, others: [34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 140 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300980 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(C)C=C(C)C(F)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 5, 1, 1, 5, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 71 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300980 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300980 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300980/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300980 Building REAL300000300981 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300981' /scratch/stefan/7770550/working/building/REAL300000300981 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300981 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300981/0 /scratch/stefan/7770550/working/building/REAL300000300981 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1439) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1439 `/scratch/stefan/7770550/working/3D/1439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1OC) `REAL300000300981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300981 none COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 48, 48, 48, 48, 48, 16, 7, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 48, 48, 60, 60, 60, 60, 48, 48, 48, 1, 1, 1, 2, 2, 2, 60, 60, 60] 60 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300981 none COC1=CC=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 48, 48, 23, 23, 48, 48, 48, 48, 48, 1, 1, 5, 4, 4, 4, 1, 1, 1, 48, 48, 48, 48, 48, 48, 5, 5, 5] 60 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300981 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300981/1 /scratch/stefan/7770550/working/building/REAL300000300981 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1440) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1440 `/scratch/stefan/7770550/working/3D/1440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1OC) `REAL300000300981.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300981 none COC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 39, 39, 39, 39, 39, 11, 7, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 39, 39, 49, 49, 49, 49, 39, 39, 39, 7, 1, 1, 1, 2, 2, 2, 49, 49, 49] 49 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300981 none COC1=CC=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 23, 39, 39, 23, 23, 39, 39, 39, 39, 39, 1, 1, 3, 4, 4, 4, 1, 1, 1, 23, 39, 39, 39, 39, 39, 39, 3, 3, 3] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 21, 22, 27, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300981 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300981 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300981/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300981/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300981 Building REAL300000300982 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300982' /scratch/stefan/7770550/working/building/REAL300000300982 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300982 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300982/0 /scratch/stefan/7770550/working/building/REAL300000300982 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1441) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1441 `/scratch/stefan/7770550/working/3D/1441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCNC(=O)C2=C1) `REAL300000300982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300982 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCNC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300982 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C2OCCNC(=O)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300982 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300982 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300982/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300982 Building REAL300000300983 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300983' /scratch/stefan/7770550/working/building/REAL300000300983 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300983 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300983/0 /scratch/stefan/7770550/working/building/REAL300000300983 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1442) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1442 `/scratch/stefan/7770550/working/3D/1442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C(C#N)=C1) `REAL300000300983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300983 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1] 17 rigid atoms, others: [32, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300983 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(Br)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 5, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([32, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300983 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300983/1 /scratch/stefan/7770550/working/building/REAL300000300983 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1443) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1443 `/scratch/stefan/7770550/working/3D/1443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)C(C#N)=C1) `REAL300000300983.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300983 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 15, 17, 17, 17, 17, 17, 9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300983 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CC=C(Br)C(C#N)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.1', 'N.1', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300983 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300983 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300983/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300983/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300983 Building REAL300000300984 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300984' /scratch/stefan/7770550/working/building/REAL300000300984 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300984 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300984/0 /scratch/stefan/7770550/working/building/REAL300000300984 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1444) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1444 `/scratch/stefan/7770550/working/3D/1444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=COC2=CC=CC=C12) `REAL300000300984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300984 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 23, 31, 31, 31, 31, 31, 23, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1] 31 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300984 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 31, 31, 31, 31, 31] 31 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300984 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300984 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300984/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300984 Building REAL300000300985 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300985' /scratch/stefan/7770550/working/building/REAL300000300985 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300985 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300985/0 /scratch/stefan/7770550/working/building/REAL300000300985 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1445) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1445 `/scratch/stefan/7770550/working/3D/1445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1OC) `REAL300000300985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300985 none COC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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, 65, 65, 65, 65, 65, 65, 19, 8, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 65, 65, 99, 99, 99, 99, 65, 65, 1, 1, 1, 2, 2, 2, 99, 99, 99] 99 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 271 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300985 none COC1=CC=C(F)C(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 28, 65, 65, 28, 28, 65, 65, 65, 65, 65, 1, 1, 4, 4, 4, 4, 1, 1, 65, 65, 65, 65, 65, 65, 5, 5, 5] 99 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 334 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300985 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300985 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300985/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300985 Building REAL300000300986 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300986' /scratch/stefan/7770550/working/building/REAL300000300986 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300986 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300986/0 /scratch/stefan/7770550/working/building/REAL300000300986 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1446) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1446 `/scratch/stefan/7770550/working/3D/1446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CCCC1) `REAL300000300986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300986 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 29, 35, 37, 37, 37, 37, 20, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 40 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300986 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 17, 17, 17, 37, 37, 37, 37, 37, 37, 40, 40, 40, 40, 2, 2, 2, 1, 1, 1, 37, 37, 37, 37, 40, 40, 40, 40, 40, 40, 40, 40, 40] 40 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300986 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 35, 40, 40, 40, 40, 40, 26, 15, 5, 15, 15, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 5, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 120 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300986 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300986 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300986/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300986 Building REAL300000300987 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300987' /scratch/stefan/7770550/working/building/REAL300000300987 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300987 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300987/0 /scratch/stefan/7770550/working/building/REAL300000300987 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1447) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1447 `/scratch/stefan/7770550/working/3D/1447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CC1) `REAL300000300987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300987 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 35, 22, 35, 35, 35, 35, 35, 22, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 6, 6, 6, 6, 6] 55 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300987 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 18, 18, 18, 35, 35, 35, 35, 35, 35, 55, 55, 2, 2, 2, 1, 1, 1, 35, 35, 35, 35, 55, 55, 55, 55, 55] 55 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300987 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 43, 55, 55, 55, 55, 55, 43, 22, 6, 22, 22, 6, 6, 6, 6, 6, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 6, 7, 7, 7, 1, 1, 1, 1, 1] 55 rigid atoms, others: [33, 34, 35, 36, 37, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 192 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300987 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300987 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300987/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300987 Building REAL300000300988 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300988' /scratch/stefan/7770550/working/building/REAL300000300988 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300988 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300988/0 /scratch/stefan/7770550/working/building/REAL300000300988 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1448) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1448 `/scratch/stefan/7770550/working/3D/1448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)F)C=C1) `REAL300000300988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300988 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 9, 9, 10, 10, 10, 10, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 9, 15, 15, 1, 1, 10, 10, 10, 10, 10, 10, 5, 1, 1, 15, 1, 1] 65 rigid atoms, others: [32, 34, 35, 11, 14, 15, 16, 17, 18, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300988 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC=C(OC(F)F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 10, 50, 65, 65, 10, 10, 2, 2, 2, 1, 1, 1, 5, 10, 10, 65, 10, 10] 65 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300988 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300988 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300988/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300988 Building REAL300000300989 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300989' /scratch/stefan/7770550/working/building/REAL300000300989 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300989 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300989/0 /scratch/stefan/7770550/working/building/REAL300000300989 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1449) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1449 `/scratch/stefan/7770550/working/3D/1449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC2=C1OCO2) `REAL300000300989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300989 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 29, 45, 46, 46, 46, 46, 29, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 1, 1, 1, 1] 46 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300989 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(F)C=CC2=C1OCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 15, 1, 1, 1, 1, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 2, 2, 1, 1, 1, 46, 46, 46, 46] 46 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300989 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300989 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300989/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300989 Building REAL300000300990 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300990' /scratch/stefan/7770550/working/building/REAL300000300990 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300990 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300990/0 /scratch/stefan/7770550/working/building/REAL300000300990 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1450) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1450 `/scratch/stefan/7770550/working/3D/1450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2N=NN(C)C2=CC=C1) `REAL300000300990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300990 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2N=NN(C)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 18, 21, 21, 21, 21, 13, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1] 21 rigid atoms, others: [33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300990 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2N=NN(C)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 1, 1, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300990 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300990/1 /scratch/stefan/7770550/working/building/REAL300000300990 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1451) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1451 `/scratch/stefan/7770550/working/3D/1451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2N=NN(C)C2=CC=C1) `REAL300000300990.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300990 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2N=NN(C)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 12, 24, 24, 24, 24, 24, 12, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 12, 2, 2, 2, 1, 1, 1] 24 rigid atoms, others: [34, 35, 36, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300990 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2N=NN(C)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 8, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 1, 1, 7, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300990 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300990 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300990/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300990/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300990 Building REAL300000300991 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300991' /scratch/stefan/7770550/working/building/REAL300000300991 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300991 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300991/0 /scratch/stefan/7770550/working/building/REAL300000300991 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1452) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1452 `/scratch/stefan/7770550/working/3D/1452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Br) `REAL300000300991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300991 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 8, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 1, 1, 2, 2, 2, 13] 13 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300991 none CC1=CC(C)=C(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 13, 13, 5, 13, 13, 13, 13, 13, 13, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 26, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300991 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300991 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300991/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300991 Building REAL300000300992 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300992' /scratch/stefan/7770550/working/building/REAL300000300992 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300992 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300992/0 /scratch/stefan/7770550/working/building/REAL300000300992 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1453) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1453 `/scratch/stefan/7770550/working/3D/1453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2C(=CC=C1)C=CN2C) `REAL300000300992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300992 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2C(=CC=C1)C=CN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 7, 11, 11, 11, 11, 11, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 2, 2, 2] 11 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300992 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2C(=CC=C1)C=CN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300992 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300992/1 /scratch/stefan/7770550/working/building/REAL300000300992 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1454) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1454 `/scratch/stefan/7770550/working/3D/1454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2C(=CC=C1)C=CN2C) `REAL300000300992.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300992 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2C(=CC=C1)C=CN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 5, 9, 9, 9, 9, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 2, 2, 2] 9 rigid atoms, others: [32, 33, 34, 35, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 60 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300992 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2C(=CC=C1)C=CN2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300992 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300992 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300992/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300992/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300992 Building REAL300000300993 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300993' /scratch/stefan/7770550/working/building/REAL300000300993 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300993 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300993/0 /scratch/stefan/7770550/working/building/REAL300000300993 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1455) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1455 `/scratch/stefan/7770550/working/3D/1455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN=C1N) `REAL300000300993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300993 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 2, 17, 17, 17] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300993 none CC1=CC(S(=O)(=O)NC2=CC=C(C(=O)[O-])C=C2C)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 16, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 9, 17, 17, 17, 17, 17, 17, 1, 1, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 35, 33, 34, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300993 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300993/1 /scratch/stefan/7770550/working/building/REAL300000300993 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1456) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1456 `/scratch/stefan/7770550/working/3D/1456' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN=C1N) `REAL300000300993.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300993 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 9, 5, 9, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 2, 17, 17, 17] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300993 none CC1=CC(S(=O)(=O)[N-]C2=CC=C(C(=O)[O-])C=C2C)=CN=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 9, 9, 17, 17, 17, 17, 17, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 1, 2, 2] 17 rigid atoms, others: [0, 1, 2, 3, 4, 32, 18, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300993 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300993 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300993/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300993/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300993 Building REAL300000300994 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300994' /scratch/stefan/7770550/working/building/REAL300000300994 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300994 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300994/0 /scratch/stefan/7770550/working/building/REAL300000300994 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1457) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1457 `/scratch/stefan/7770550/working/3D/1457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NSC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C) `REAL300000300994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300994 none COC1=NSC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 15, 7, 15, 15, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 35, 35, 35, 35, 1, 1, 1, 2, 2, 2] 35 rigid atoms, others: [10, 11, 12, 13, 14, 15, 18, 19, 20, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300994 none COC1=NSC=C1S(=O)(=O)[N-]C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 35, 35, 21, 21, 35, 35, 35, 35, 35, 4, 4, 4, 1, 35, 35, 35, 35, 35, 35] 35 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 24] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300994 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300994 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300994/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300994 Building REAL300000300995 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300995' /scratch/stefan/7770550/working/building/REAL300000300995 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300995 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300995/0 /scratch/stefan/7770550/working/building/REAL300000300995 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1458) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1458 `/scratch/stefan/7770550/working/3D/1458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCCC(C)(C)C1) `REAL300000300995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300995 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCCC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 18 rigid atoms, others: [32, 33, 34, 41, 42, 11, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40]) total number of confs: 60 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300995 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)N1CCCC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1, 1, 1, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300995 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300995 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300995/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300995 Building REAL300000300996 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300996' /scratch/stefan/7770550/working/building/REAL300000300996 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300996 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300996/0 /scratch/stefan/7770550/working/building/REAL300000300996 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1459) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1459 `/scratch/stefan/7770550/working/3D/1459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC(F)=CC(Cl)=C2OC1) `REAL300000300996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300996 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC(F)=CC(Cl)=C2OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 32, 43, 43, 43, 43, 43, 27, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 27, 1, 1, 1, 1, 1] 43 rigid atoms, others: [33, 34, 35, 36, 37, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 166 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300996 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC2=CC(F)=CC(Cl)=C2OC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 15, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 19, 19, 19, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 1, 1, 1, 8, 43, 43, 43, 43, 43] 43 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300996 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300996 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300996/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300996 Building REAL300000300997 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300997' /scratch/stefan/7770550/working/building/REAL300000300997 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000300997 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300997/0 /scratch/stefan/7770550/working/building/REAL300000300997 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1460) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1460 `/scratch/stefan/7770550/working/3D/1460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2C=COC2=C(F)C=C1) `REAL300000300997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300997 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 19, 27, 27, 27, 27, 27, 19, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 19, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 106 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300997 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 2, 1, 1, 1, 7, 27, 27, 27, 27] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300997 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000300997/1 /scratch/stefan/7770550/working/building/REAL300000300997 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1461) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1461 `/scratch/stefan/7770550/working/3D/1461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2C=COC2=C(F)C=C1) `REAL300000300997.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000300997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300997 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 21, 21, 29, 29, 29, 29, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 24, 25, 26, 27, 28, 29]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300997 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C2C=COC2=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 29, 29, 29, 29] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 27, 28, 29] set([32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300997 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300997 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000300997/1.* 0: /scratch/stefan/7770550/working/building/REAL300000300997/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300997 Building REAL300000300998 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300998' /scratch/stefan/7770550/working/building/REAL300000300998 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300998 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300998/0 /scratch/stefan/7770550/working/building/REAL300000300998 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1462) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1462 `/scratch/stefan/7770550/working/3D/1462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CCC1) `REAL300000300998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300998 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 22, 35, 39, 39, 39, 39, 22, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6] 51 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300998 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 15, 15, 15, 39, 39, 39, 39, 39, 39, 51, 51, 51, 2, 2, 2, 1, 1, 1, 39, 39, 39, 39, 51, 51, 51, 51, 51, 51, 51] 51 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 140 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: REAL300000300998 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=CN(C)N=C1C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 37, 51, 51, 51, 51, 51, 37, 17, 6, 17, 17, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1] 51 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 185 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300998 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300998 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300998/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300998 Building REAL300000300999 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000300999' /scratch/stefan/7770550/working/building/REAL300000300999 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300000300999 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000300999/0 /scratch/stefan/7770550/working/building/REAL300000300999 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1463) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1463 `/scratch/stefan/7770550/working/3D/1463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(C)C)=CC=C1C(C)C) `REAL300000300999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000300999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000300999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300999 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(C)C)=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 9, 13, 13, 13, 13, 5, 3, 1, 3, 3, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 2, 2, 13, 13, 13, 13, 13, 13, 5, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 2] 18 rigid atoms, others: [33, 41, 42, 11, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 91 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000300999 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=CC(C(C)C)=CC=C1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 18, 18, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 6, 13, 18, 18, 18, 18, 18, 18, 18, 13, 13, 13, 13, 13, 13, 13, 13, 13] 18 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000300999 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000300999 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 0: /scratch/stefan/7770550/working/building/REAL300000300999/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000300999 Building REAL300000301000 mkdir: created directory `/scratch/stefan/7770550/working/building/REAL300000301000' /scratch/stefan/7770550/working/building/REAL300000301000 /scratch/stefan/7770550/working /scratch/stefan/7770550 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300000301000 mkdir: created directory `0' /scratch/stefan/7770550/working/building/REAL300000301000/0 /scratch/stefan/7770550/working/building/REAL300000301000 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 0 (index: 1464) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1464 `/scratch/stefan/7770550/working/3D/1464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)SC=C1) `REAL300000301000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300000301000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000301000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000301000 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 10, 19, 19, 19, 19, 19, 10, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000301000 none CC1=CC(C(=O)[O-])=CC=C1[N-]S(=O)(=O)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 23, 24, 25] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000301000 /scratch/stefan/7770550/working /scratch/stefan/7770550 mkdir: created directory `1' /scratch/stefan/7770550/working/building/REAL300000301000/1 /scratch/stefan/7770550/working/building/REAL300000301000 /scratch/stefan/7770550/working /scratch/stefan/7770550 Protomer 1 (index: 1465) Found valid previously generated 3D confromation in /scratch/stefan/7770550/working/3D/1465 `/scratch/stefan/7770550/working/3D/1465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(Cl)SC=C1) `REAL300000301000.mol2' -> `1.mol2' `temp.mol2' -> `REAL300000301000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770550/working/building/REAL300000301000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000301000 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 9, 9, 19, 19, 19, 19, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1] 19 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300000301000 none CC1=CC(C(=O)[O-])=CC=C1NS(=O)(=O)C1=C(Cl)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 8, 14, 11, 11, 1, 1, 16, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770550/working/building/REAL300000301000 /scratch/stefan/7770550/working /scratch/stefan/7770550 Finished preparing REAL300000301000 Recording results /scratch/stefan/7770550/working /scratch/stefan/7770550 Appending to /scratch/stefan/7770550/finished/xaaaaaa.* 1: /scratch/stefan/7770550/working/building/REAL300000301000/1.* 0: /scratch/stefan/7770550/working/building/REAL300000301000/0.* Removing working files in /scratch/stefan/7770550/working/building/REAL300000301000 /scratch/stefan/7770550 Compressing combined databse files /scratch/stefan/7770550/finished/xaaaaaa.db2.gz /scratch/stefan/7770550/finished/xaaaaaa.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7770550/finished) ======================================================= Finalizing... removed `/scratch/stefan/7770550/working/3D/1466' removed directory: `/scratch/stefan/7770550/working/3D' `/scratch/stefan/7770550/working/protonate' -> `/scratch/stefan/7770550/archive' `/scratch/stefan/7770550/working/input-smiles.ism' -> `/scratch/stefan/7770550/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7770550/working/building' rmdir: removing directory, `/scratch/stefan/7770550/working' ls: No match. ls: No match.